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<h3>
Alexandre Mestiashvili pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/bowtie2">Debian Med / bowtie2</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/bowtie2/commit/157dbc209f47672a9a7167d16e3a324803906000">157dbc20</a></strong>
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<span>by Alexandre Mestiashvili</span>
<i>at 2018-08-14T09:16:33Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2.3.4.2</pre>
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<h4>26 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9a2aa4db38d3115ed60da621e012c0efc0172aae">
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+
CMakeLists.txt
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</li>
<li class="file-stats">
<a href="#f11fb3bba37e7060bedcd5895812b7c511c52651">
MANUAL
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<li class="file-stats">
<a href="#465370da702349b6dcb3f9f2026872cad6877efa">
MANUAL.markdown
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<li class="file-stats">
<a href="#836efb6e25a091dcb4ff8e1dbb2f0be6a5cbf14c">
Makefile
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<li class="file-stats">
<a href="#9f621eb5fd3bcb2fa5c7bd228c9b1ad42edc46c8">
NEWS
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<li class="file-stats">
<a href="#b33892fbddeffc3368077b4904ad0b3d562a7312">
VERSION
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<li class="file-stats">
<a href="#057e0784d807c7b84958635ddeeb5003f2751ece">
aln_sink.cpp
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<li class="file-stats">
<a href="#464ce98392db4e108605b7a12696e7c3434eaf56">
bowtie2-build
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<li class="file-stats">
<a href="#622d3bcfba0df0e4ae8a0849416ed2d2cf987528">
bowtie2-inspect
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<li class="file-stats">
<a href="#d1904db8401bf0137951f60c3d4a34a7cf8e2e84">
bt2_idx.h
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<li class="file-stats">
<a href="#6026283a643bf7fb08c2ef0b797486df93cf0698">
bt2_search.cpp
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<a href="#ccc364c6c660e798a4f3c3b78119cbea257aee1e">
doc/manual.html
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<a href="#a1ba375e8deab5b12b1347797835e927dca95425">
doc/website/manual.ssi
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<a href="#9485aa1b2c39982f48264019fde0712132ed80f5">
doc/website/recent_news.ssi
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<a href="#59bf596910fb7006481a4d8a45de81ff2bd75a4d">
doc/website/rhsidebar.ssi
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<a href="#f33859afffab10e65cd96fbe0811935a2f3508a1">
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example/reads/combined_reads.bam
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<li class="file-stats">
<a href="#ca0679d32b003b8024f4d51789e4d6e5b06db9c9">
formats.h
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<li class="file-stats">
<a href="#50b0e95b63ccb2c46e008fda8904d780b714df41">
opts.h
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<li class="file-stats">
<a href="#7c4ae52e4a13c990d16c9530fb874ed79064a5cd">
pat.cpp
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<a href="#6c8922e214bc665a49b5acea11b505cbd36446c5">
pat.h
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<li class="file-stats">
<a href="#9fc1681b02d842aa2b7bb9db116eff864b181fdf">
presets.cpp
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<li class="file-stats">
<a href="#c297ba4595a07ed6c1a79135075b7b1f5e55a14c">
read.h
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<li class="file-stats">
<a href="#66965a83f981ce6b0882f308dd88614650b6582c">
ref_read.cpp
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<li class="file-stats">
<a href="#8cb73317275ca3f68e13f1344310abe501fa6653">
sam.cpp
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<li class="file-stats">
<a href="#7398ca21ea2a2c7a38ca176ea1edaeb67b9ca8c0">
sam.h
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<li class="file-stats">
<a href="#54bdc2e95dbd86d93a56d1f6445a8c2f9c6bedfb">
scripts/test/simple_tests.pl
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<h4>Changes:</h4>
<li id="9a2aa4db38d3115ed60da621e012c0efc0172aae">
<a href="https://salsa.debian.org/med-team/bowtie2/commit/157dbc209f47672a9a7167d16e3a324803906000#9a2aa4db38d3115ed60da621e012c0efc0172aae"><strong>CMakeLists.txt</strong></a>
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<td class="diff-line-num new new_line" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">cmake_minimum_required</span><span class="p">(</span>VERSION 2.8<span class="p">)</span> </span>
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<td class="diff-line-num new new_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="cmake"></span>
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<td class="diff-line-num new new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">cmake_policy</span><span class="p">(</span>SET CMP0048 NEW<span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">cmake_policy</span><span class="p">(</span>SET CMP0005 NEW<span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="cmake"></span>
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<td class="diff-line-num new new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">project</span><span class="p">(</span>bowtie2 LANGUAGES CXX VERSION <span class="s2" style="color: #d14;">"2.3.4.2"</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="cmake"></span>
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<td class="diff-line-num new new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">enable_testing</span><span class="p">()</span></span>
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<td class="diff-line-num new new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="cmake"></span>
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<td class="diff-line-num new new_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">include</span><span class="p">(</span>CTest<span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">include</span><span class="p">(</span>ProcessorCount<span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">include</span><span class="p">(</span>CheckSymbolExists<span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="cmake"></span>
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<td class="diff-line-num new new_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="cmake"><span class="nf" style="color: #900; font-weight: 600;">ProcessorCount</span><span class="p">(</span>NUM_CORES<span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="cmake"></span>
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<td class="diff-line-num new new_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">option</span><span class="p">(</span>BOWTIE_MM <span class="s2" style="color: #d14;">"enable bowtie2 memory mapping"</span> ON<span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">option</span><span class="p">(</span>BOWITE_SHARED_MM <span class="s2" style="color: #d14;">"enable shared memory mapping"</span> ON<span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="cmake"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">set</span><span class="p">(</span>CMAKE_CXX_STANDARD 98<span class="p">)</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">set</span><span class="p">(</span>NO_TBB <span class="si" style="color: #d14;">${</span><span class="nv" style="color: teal;">NO_TBB</span><span class="si" style="color: #d14;">}</span><span class="p">)</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">set</span><span class="p">(</span>NO_SPINLOCK, <span class="si" style="color: #d14;">${</span><span class="nv" style="color: teal;">NO_SPINLOCK</span><span class="si" style="color: #d14;">}</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">set</span><span class="p">(</span>WITH_THREAD_PROFILING <span class="si" style="color: #d14;">${</span><span class="nv" style="color: teal;">WITH_THREAD_PROFILING</span><span class="si" style="color: #d14;">}</span><span class="p">)</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">set</span><span class="p">(</span>POPCNT_CAPABILITY <span class="si" style="color: #d14;">${</span><span class="nv" style="color: teal;">POPCNT_CAPABILITY</span><span class="si" style="color: #d14;">}</span><span class="p">)</span></span>
</pre>
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<td class="diff-line-num new old_line" 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="diff-line-num new new_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
24
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC24" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">set</span><span class="p">(</span>CMAKE_CXX_FLAGS <span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: teal;">CMAKE_CXX_FLAGS</span><span class="si" style="color: #d14;">}</span><span class="s2" style="color: #d14;"> -m64 -g3 -Wall -msse2"</span><span class="p">)</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
25
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC25" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">set</span><span class="p">(</span>CMAKE_CXX_FLAGS_DEBUG <span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: teal;">CMAKE_CXX_FLAGS_DEBUG</span><span class="si" style="color: #d14;">}</span><span class="s2" style="color: #d14;"> -O0"</span><span class="p">)</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
26
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC26" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">set</span><span class="p">(</span>CMAKE_CXX_FLAGS_RELEASE <span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: teal;">CMAKE_CXX_FLAGS_RELEASE</span><span class="si" style="color: #d14;">}</span><span class="s2" style="color: #d14;"> -O3 -funroll-loops"</span><span class="p">)</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">set</span><span class="p">(</span>INSTALL_DIR <span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: teal;">CMAKE_INSTALL_PREFIX</span><span class="si" style="color: #d14;">}</span><span class="s2" style="color: #d14;">/bin"</span> CACHE PATH <span class="s2" style="color: #d14;">"Installation directory for executables"</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="cmake"></span>
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<td class="diff-line-num new new_line" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">set</span><span class="p">(</span>CMAKE_EXPORT_COMPILE_COMMANDS on<span class="p">)</span></span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="cmake"></span>
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<td class="diff-line-num new new_line" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">if</span> <span class="p">(</span>MINGW<span class="p">)</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">option</span><span class="p">(</span>BOWTIE_MM <span class="s2" style="color: #d14;">"Memory mapped files not supported on Windows"</span> OFF<span class="p">)</span></span>
</pre>
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<td class="diff-line-num new old_line" 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="diff-line-num new new_line" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">option</span><span class="p">(</span>BOWTIE_SHARED_MEM <span class="s2" style="color: #d14;">"Shared memory not supported on Windows"</span> OFF<span class="p">)</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">endif</span><span class="p">(</span>MINGW<span class="p">)</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="35" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="cmake"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">if</span> <span class="p">(</span>APPLE<span class="p">)</span></span>
</pre>
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<td class="diff-line-num new old_line" 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="diff-line-num new new_line" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">set</span><span class="p">(</span>CMAKE_XCODE_ATTRIBUTE_DEBUG_INFORMATION_FORMAT <span class="s2" style="color: #d14;">"dwarf-with-dsym"</span><span class="p">)</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">endif</span><span class="p">(</span>APPLE<span class="p">)</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="cmake"></span>
</pre>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">set</span><span class="p">(</span>BOWTIE2_BIN_LIST</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="cmake"> bowtie2-build-s</span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="cmake"> bowtie2-build-l</span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="cmake"> bowtie2-align-s</span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="cmake"> bowtie2-align-l</span>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="cmake"> bowtie2-inspect-s</span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="cmake"> bowtie2-inspect-l</span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="cmake"> <span class="p">)</span></span>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="cmake"></span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">set</span><span class="p">(</span>SHARED_CPPS</span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="cmake"> ccnt_lut.cpp</span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="cmake"> ref_read.cpp</span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="cmake"> alphabet.cpp</span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="cmake"> shmem.cpp</span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="cmake"> edit.cpp</span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="cmake"> bt2_idx.cpp</span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="cmake"> bt2_io.cpp</span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="cmake"> bt2_util.cpp</span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="cmake"> reference.cpp</span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="cmake"> ds.cpp</span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="cmake"> multikey_qsort.cpp</span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="cmake"> limit.cpp</span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="cmake"> random_source.cpp</span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="cmake"> <span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="cmake"></span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">set</span><span class="p">(</span>SEARCH_CPPS</span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="cmake"> qual.cpp pat.cpp sam.cpp</span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="cmake"> read_qseq.cpp aligner_seed_policy.cpp </span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="cmake"> aligner_seed.cpp </span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="cmake"> aligner_seed2.cpp </span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="cmake"> aligner_sw.cpp </span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="cmake"> aligner_sw_driver.cpp aligner_cache.cpp </span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="cmake"> aligner_result.cpp ref_coord.cpp mask.cpp </span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="cmake"> pe.cpp aln_sink.cpp dp_framer.cpp </span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="cmake"> scoring.cpp presets.cpp unique.cpp </span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="cmake"> simple_func.cpp </span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="cmake"> random_util.cpp </span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="cmake"> aligner_bt.cpp sse_util.cpp </span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="cmake"> aligner_swsse.cpp outq.cpp </span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="cmake"> aligner_swsse_loc_i16.cpp </span>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="cmake"> aligner_swsse_ee_i16.cpp </span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="cmake"> aligner_swsse_loc_u8.cpp </span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="cmake"> aligner_swsse_ee_u8.cpp </span>
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="cmake"> aligner_driver.cpp</span>
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="cmake"> bowtie_main.cpp</span>
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="cmake"> bt2_search.cpp</span>
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="cmake"> <span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="cmake"></span>
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">set</span><span class="p">(</span>BUILD_CPPS</span>
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="cmake"> bt2_build.cpp</span>
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="cmake"> diff_sample.cpp</span>
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="cmake"> bowtie_build_main.cpp<span class="p">)</span></span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="cmake"></span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">set</span><span class="p">(</span>INSPECT_CPPS</span>
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="cmake"> bt2_inspect.cpp </span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="cmake"> <span class="p">)</span></span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="cmake"></span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">string</span><span class="p">(</span>TIMESTAMP BUILD_DATE<span class="p">)</span></span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">execute_process</span><span class="p">(</span>COMMAND <span class="si" style="color: #d14;">${</span><span class="nv" style="color: teal;">CMAKE_CXX_COMPILER</span><span class="si" style="color: #d14;">}</span> -v OUTPUT_VARIABLE COMPILER_VERSION<span class="p">)</span></span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="cmake"></span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">add_definitions</span><span class="p">(</span></span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="cmake"> -DBOWTIE2</span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="cmake"> -DBUILD_HOST=<span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: teal;">CMAKE_HOST_SYSTEM</span><span class="si" style="color: #d14;">}</span><span class="s2" style="color: #d14;">"</span></span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="cmake"> -DBUILD_TIME=<span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: teal;">BUILD_DATE</span><span class="si" style="color: #d14;">}</span><span class="s2" style="color: #d14;">"</span></span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="cmake"> -DCOMPILER_VERSION=<span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: teal;">CMAKE_CXX_COMPILER</span><span class="si" style="color: #d14;">}</span><span class="s2" style="color: #d14;"> </span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: teal;">CMAKE_CXX_COMPILER_VERSION</span><span class="si" style="color: #d14;">}</span><span class="s2" style="color: #d14;">"</span></span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="cmake"> -DBOWTIE2_VERSION=<span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: teal;">PROJECT_VERSION</span><span class="si" style="color: #d14;">}</span><span class="s2" style="color: #d14;">"</span></span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="cmake"> -D_LARGEFILE_SOURCE</span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="cmake"> -D_FILE_OFFSET_BITS=64</span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="cmake"> -D_GNU_SOURCE</span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="cmake"> <span class="p">)</span></span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="cmake"></span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">if</span> <span class="p">(</span>WITH_AFFINITY<span class="p">)</span></span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">add_definitions</span><span class="p">(</span>-DWITH_AFFINITY=1<span class="p">)</span></span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">endif</span><span class="p">()</span></span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="cmake"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="115" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">if</span> <span class="p">(</span>NO_SPINLOCK<span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="116" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">add_definitions</span><span class="p">(</span>-DNO_SPINLOCK<span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="117" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">endif</span><span class="p">()</span></span>
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<td class="diff-line-num new new_line" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="cmake"></span>
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<td class="diff-line-num new new_line" data-linenumber="119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">if</span> <span class="p">(</span>POPCNT_CAPABILITY<span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="120" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">add_definitions</span><span class="p">(</span>-DPOPCNT_CAPABILITY<span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="121" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">set</span><span class="p">(</span>CMAKE_CXX_FLAGS <span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: teal;">CMAKE_CXX_FLAGS</span><span class="si" style="color: #d14;">}</span><span class="s2" style="color: #d14;"> -I third_party"</span><span class="p">)</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="122" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">endif</span><span class="p">()</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="123" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="cmake"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="124" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">if</span> <span class="p">(</span>WITH_THREAD_PROFILING<span class="p">)</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="125" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">add_definitions</span><span class="p">(</span>-DPER_THREAD_TIMING=1<span class="p">)</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">endif</span><span class="p">()</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="cmake"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">if</span> <span class="p">(</span>CMAKE_BUILD_TYPE STREQUAL <span class="s2" style="color: #d14;">"Release"</span><span class="p">)</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">add_definitions</span><span class="p">(</span>-DNDEBUG<span class="p">)</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">endif</span><span class="p">()</span></span>
</pre>
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<td class="diff-line-num new new_line" 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="cmake"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">find_package</span><span class="p">(</span>Threads REQUIRED<span class="p">)</span></span>
</pre>
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<td class="diff-line-num new old_line" 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="diff-line-num new new_line" data-linenumber="133" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">find_package</span><span class="p">(</span>ZLIB REQUIRED<span class="p">)</span></span>
</pre>
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<td class="diff-line-num new old_line" 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="diff-line-num new new_line" data-linenumber="134" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">find_path</span><span class="p">(</span>TBB_INCLUDE_PATH tbb<span class="p">)</span></span>
</pre>
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<td class="diff-line-num new old_line" 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="diff-line-num new new_line" data-linenumber="135" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">find_library</span><span class="p">(</span>TBB_LIBRARY_PATH tbb<span class="p">)</span></span>
</pre>
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<td class="diff-line-num new old_line" 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="diff-line-num new new_line" data-linenumber="136" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">find_library</span><span class="p">(</span>TBB_MALLOC_LIBRARY_PATH tbbmalloc<span class="p">)</span></span>
</pre>
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<td class="diff-line-num new old_line" 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="diff-line-num new new_line" data-linenumber="137" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="cmake"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="138" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">if</span> <span class="p">(</span>ZLIB_FOUND<span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="139" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">link_libraries</span><span class="p">(</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: teal;">ZLIB_LIBRARIES</span><span class="si" style="color: #d14;">}</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="140" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">include_directories</span><span class="p">(</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: teal;">ZLIB_INCLUDE_DIRS</span><span class="si" style="color: #d14;">}</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">endif</span><span class="p">()</span></span>
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<td class="diff-line-num new new_line" data-linenumber="142" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="cmake"></span>
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<td class="diff-line-num new new_line" data-linenumber="143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">if</span> <span class="p">(</span>Threads_FOUND<span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="144" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">link_libraries</span><span class="p">(</span>Threads::Threads<span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="145" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">endif</span><span class="p">()</span></span>
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<td class="diff-line-num new new_line" data-linenumber="146" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="cmake"></span>
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<td class="diff-line-num new new_line" data-linenumber="147" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">if</span> <span class="p">(</span>NOT TBB_LIBRARY_PATH<span class="p">)</span></span>
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<td class="diff-line-num new new_line" 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="cmake"> <span class="nb" style="color: #0086b3;">set</span><span class="p">(</span>SHARED_CPPS <span class="si" style="color: #d14;">${</span><span class="nv" style="color: teal;">SHARED_CPPS</span><span class="si" style="color: #d14;">}</span> tinythread.cpp<span class="p">)</span></span>
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<td class="diff-line-num new new_line" 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="cmake"><span class="nb" style="color: #0086b3;">else</span><span class="p">()</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="150" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">if</span> <span class="p">(</span>NOT NO_QUEUELOCK<span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="151" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">add_definitions</span><span class="p">(</span>-DWITH_TBB -DWITH_QUEUELOCK=1 -DNO_SPINLOCK<span class="p">)</span></span>
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<td class="diff-line-num new new_line" 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="cmake"> <span class="nb" style="color: #0086b3;">endif</span><span class="p">()</span></span>
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<td class="diff-line-num new new_line" data-linenumber="153" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">include_directories</span><span class="p">(</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: teal;">TBB_INCLUDE_PATH</span><span class="si" style="color: #d14;">}</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="154" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">link_libraries</span><span class="p">(</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: teal;">TBB_LIBRARY_PATH</span><span class="si" style="color: #d14;">}</span> <span class="si" style="color: #d14;">${</span><span class="nv" style="color: teal;">TBB_MALLOC_LIBRARY_PATH</span><span class="si" style="color: #d14;">}</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="155" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">endif</span><span class="p">()</span></span>
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<td class="diff-line-num new new_line" data-linenumber="156" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="cmake"></span>
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<td class="diff-line-num new new_line" data-linenumber="157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">include_directories</span><span class="p">(</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: teal;">PROJECT_SOURCE_DIR</span><span class="si" style="color: #d14;">}</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="158" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">get_directory_property</span><span class="p">(</span>COMPILER_DEFS COMPILE_DEFINITIONS<span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">add_definitions</span><span class="p">(</span>-DCOMPILER_OPTIONS=<span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: teal;">CMAKE_CXX_FLAGS</span><span class="si" style="color: #d14;">}</span><span class="s2" style="color: #d14;">"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="cmake"></span>
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161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">add_executable</span><span class="p">(</span>bowtie2-align-s <span class="si" style="color: #d14;">${</span><span class="nv" style="color: teal;">SEARCH_CPPS</span><span class="si" style="color: #d14;">}</span> <span class="si" style="color: #d14;">${</span><span class="nv" style="color: teal;">SHARED_CPPS</span><span class="si" style="color: #d14;">}</span><span class="p">)</span></span>
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162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">add_executable</span><span class="p">(</span>bowtie2-align-l <span class="si" style="color: #d14;">${</span><span class="nv" style="color: teal;">SEARCH_CPPS</span><span class="si" style="color: #d14;">}</span> <span class="si" style="color: #d14;">${</span><span class="nv" style="color: teal;">SHARED_CPPS</span><span class="si" style="color: #d14;">}</span><span class="p">)</span></span>
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163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">add_executable</span><span class="p">(</span>bowtie2-build-s <span class="si" style="color: #d14;">${</span><span class="nv" style="color: teal;">BUILD_CPPS</span><span class="si" style="color: #d14;">}</span> <span class="si" style="color: #d14;">${</span><span class="nv" style="color: teal;">SHARED_CPPS</span><span class="si" style="color: #d14;">}</span><span class="p">)</span></span>
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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">add_executable</span><span class="p">(</span>bowtie2-build-l <span class="si" style="color: #d14;">${</span><span class="nv" style="color: teal;">BUILD_CPPS</span><span class="si" style="color: #d14;">}</span> <span class="si" style="color: #d14;">${</span><span class="nv" style="color: teal;">SHARED_CPPS</span><span class="si" style="color: #d14;">}</span><span class="p">)</span></span>
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165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">add_executable</span><span class="p">(</span>bowtie2-inspect-s <span class="si" style="color: #d14;">${</span><span class="nv" style="color: teal;">INSPECT_CPPS</span><span class="si" style="color: #d14;">}</span> <span class="si" style="color: #d14;">${</span><span class="nv" style="color: teal;">SHARED_CPPS</span><span class="si" style="color: #d14;">}</span><span class="p">)</span></span>
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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">add_executable</span><span class="p">(</span>bowtie2-inspect-l <span class="si" style="color: #d14;">${</span><span class="nv" style="color: teal;">INSPECT_CPPS</span><span class="si" style="color: #d14;">}</span> <span class="si" style="color: #d14;">${</span><span class="nv" style="color: teal;">SHARED_CPPS</span><span class="si" style="color: #d14;">}</span><span class="p">)</span></span>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="cmake"></span>
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168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">set_target_properties</span><span class="p">(</span>bowtie2-align-l bowtie2-build-l bowtie2-inspect-l PROPERTIES COMPILE_FLAGS <span class="s2" style="color: #d14;">"-DBOWTIE2_64BIT_INDEX"</span><span class="p">)</span></span>
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">set_target_properties</span><span class="p">(</span>bowtie2-inspect-s bowtie2-inspect-l PROPERTIES COMPILE_FLAGS <span class="s2" style="color: #d14;">"-DBOWTIE_INSPECT_MAIN"</span><span class="p">)</span></span>
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170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">set_target_properties</span><span class="p">(</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: teal;">BOWTIE2_BIN_LIST</span><span class="si" style="color: #d14;">}</span> PROPERTIES DEBUG_POSTFIX <span class="s2" style="color: #d14;">"-debug"</span><span class="p">)</span></span>
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171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="cmake"></span>
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<td class="diff-line-num new new_line" data-linenumber="172" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">add_test</span><span class="p">(</span>NAME simple-align COMMAND <span class="si" style="color: #d14;">${</span><span class="nv" style="color: teal;">PROJECT_SOURCE_DIR</span><span class="si" style="color: #d14;">}</span>/bowtie2 -x example/index/lambda_virus example/reads/longreads.fq<span class="p">)</span></span></pre>
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<li id="f11fb3bba37e7060bedcd5895812b7c511c52651">
<a href="https://salsa.debian.org/med-team/bowtie2/commit/157dbc209f47672a9a7167d16e3a324803906000#f11fb3bba37e7060bedcd5895812b7c511c52651"><strong>MANUAL</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -3,33 +3,35 @@</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="plaintext">INTRODUCTION</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="plaintext"></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="plaintext"></span>
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6
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext">What is Bowtie 2?</span>
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7
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext"></span>
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8
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Bowtie 2 is an ultrafast and memory-efficient tool for aligning</span>
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9
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7
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">sequencing reads to long reference sequences. It is particularly good at</span>
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10
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext">aligning reads of about 50 up to 100s o<span class="idiff left right">r 1,000s of characters to</span></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext"><span class="idiff left right">relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome</span></span>
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12
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext"><span class="idiff left right">with an FM Index (based on the Burrows-Wheeler Transform or BWT) to keep</span></span>
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13
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext"><span class="idiff left right">its memory footprint small: for the human genome, its memory footprint</span></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext"><span class="idiff left right">is typically around 3.2 gigabytes of RAM. Bowtie 2 supports gapped,</span></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="plaintext"><span class="idiff left right">local, and </span>paired-end alignment modes. Multiple processors can be used</span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="plaintext">simultaneously to achieve greater alignment speed.<span class="idiff left right"> Cufflinks: a tool for</span></span>
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17
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="plaintext"><span class="idiff left right">transcriptome assembly and isoform quantitiation from Bowtie 2 outputs</span></span>
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18
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="plaintext"><span class="idiff left right">alignments in SAM format, enabling interoperation with a large number of</span></span>
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19
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="plaintext"><span class="idiff left right">other tools (e.g. SAMtools, GATK) that use SAM. Bowtie 2 is distributed</span></span>
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20
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="plaintext"><span class="idiff left right">under the GPLv3 license, and it runs on the command line under Windows,</span></span>
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21
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="plaintext">Mac OS X and Linux.</span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">aligning reads of about 50 up to 100s o<span class="idiff left right">f characters to relatively long</span></span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"><span class="idiff left right">(e.g. mammalian) genomes. Bowtie 2 indexes the genome with an FM Index</span></span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"><span class="idiff left right">(based on the Burrows-Wheeler Transform or BWT) to keep its memory</span></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"><span class="idiff left right">footprint small: for the human genome, its memory footprint is typically</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"><span class="idiff left right">around 3.2 gigabytes of RAM. Bowtie 2 supports gapped, local, and</span></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">paired-end alignment modes. Multiple processors can be used</span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">simultaneously to achieve greater alignment speed.</span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"><span class="idiff left right">Bowtie 2 outputs alignments in SAM format, enabling interoperation with</span></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"><span class="idiff left right">a large number of other tools (e.g. SAMtools, GATK) that use SAM. Bowtie</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"><span class="idiff left right">2 is distributed under the GPLv3 license, and it runs on the command</span></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"><span class="idiff left right">line under Windows, </span>Mac OS X and Linux.</span>
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22
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20
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext">Bowtie 2 is often the first step in pipelines for comparative genomics,</span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext">including for variation calling, ChIP-seq, RNA-seq, BS-seq. Bowtie 2 and</span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext">Bowtie (also called “Bowtie 1” here) are also tightly integrated into</span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="plaintext"><span class="idiff left right">some tools, including TopHat: a fast splice junction mapper for RNA-seq</span></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="plaintext"><span class="idiff left right">reads, RNA-seq reads, Crossbow: a cloud-enabled software tool for</span></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="plaintext"><span class="idiff left right">analyzing resequencing data, and Myrna: a cloud-enabled software tool</span></span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="plaintext"><span class="idiff left right">for aligning RNA-seq reads and measuring differential gene expression.</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"><span class="idiff left right">many other tools, some of which are listed here.</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext"><span class="idiff left right">If you use Bowtie 2 for your published research, please cite our work.</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext"><span class="idiff left right">Papers describing Bowtie 2 are:</span></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="plaintext">If you use Bowtie 2 for your published research, please cite the Bowtie</span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="plaintext">paper. Thank you!</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">- Langmead B, Wilks C, Antonescu V, Charles R. Scaling read aligners</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext"> to hundreds of threads on general-purpose processors.</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext"> _Bioinformatics_. 2018 Jul 18. doi: 10.1093/bioinformatics/bty648.</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">- Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2.</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext"> _Nature Methods_. 2012 Mar 4;9(4):357-9. doi: 10.1038/nmeth.1923.</span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="plaintext">How is Bowtie 2 different from Bowtie 1?</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">@@ -86,38 +88,30 @@ Bowtie 1’s.</td>
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC89" class="line" lang="plaintext">What isn’t Bowtie 2?</span>
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC89" class="line" lang="plaintext">Bowtie 1 and Bowtie 2 are not general-purpose alignment tools like</span>
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90
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<pre style="margin: 0;">-<span id="LC90" class="line" lang="plaintext">MUMmer, BLAST or Vmatch. Bowtie 2 works best when aligning to large</span>
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91
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<pre style="margin: 0;">-<span id="LC91" class="line" lang="plaintext">genomes, though it supports arbitrarily small reference sequences</span>
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92
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<pre style="margin: 0;">-<span id="LC92" class="line" lang="plaintext">(e.g. amplicons). It handles very long reads (i.e. upwards of 10s or</span>
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93
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<pre style="margin: 0;">-<span id="LC93" class="line" lang="plaintext">100s of kilobases), but it is optimized for the read lengths and error</span>
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94
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<pre style="margin: 0;">-<span id="LC94" class="line" lang="plaintext">modes yielded by recent sequencers, such as the Illumina HiSeq 2000,</span>
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95
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<pre style="margin: 0;">-<span id="LC95" class="line" lang="plaintext">Roche 454, and Ion Torrent instruments.</span>
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<pre style="margin: 0;">-<span id="LC96" class="line" lang="plaintext"></span>
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97
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<pre style="margin: 0;">-<span id="LC97" class="line" lang="plaintext">If your goal is to align two very large sequences (e.g. two genomes),</span>
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98
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<pre style="margin: 0;">-<span id="LC98" class="line" lang="plaintext">consider using MUMmer. If your goal is very sensitive alignment to a</span>
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<pre style="margin: 0;">-<span id="LC99" class="line" lang="plaintext">relatively short reference sequence (e.g. a bacterial genome), this can</span>
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<pre style="margin: 0;">-<span id="LC100" class="line" lang="plaintext">be done with Bowtie 2 but you may want to consider using tools like</span>
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<pre style="margin: 0;">-<span id="LC101" class="line" lang="plaintext">NUCmer, BLAT, or BLAST. These tools can be extremely slow when the</span>
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<pre style="margin: 0;">-<span id="LC102" class="line" lang="plaintext">reference genome is long, but are often adequate when the reference is</span>
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<pre style="margin: 0;">-<span id="LC103" class="line" lang="plaintext">short.</span>
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="plaintext">Bowtie 2 is geared toward aligning relatively short sequencing reads to</span>
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="plaintext">long genomes. That said, it handles arbitrarily small reference</span>
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="plaintext">sequences ( e.g. amplicons) and very long reads (i.e. upwards of 10s or</span>
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="plaintext">100s of kilobases), though it is slower in those settings. It is</span>
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="plaintext">optimized for the read lengths and error modes yielded by typical</span>
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="plaintext">Illumina sequencers.</span>
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104
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<pre style="margin: 0;"> <span id="LC97" class="line" lang="plaintext"></span>
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105
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<pre style="margin: 0;">-<span id="LC105" class="line" lang="plaintext">Bowtie 2 does not support alignment of colorspace reads.</span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="plaintext">Bowtie 2 does not support alignment of colorspace reads. (Bowtie 1</span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="plaintext">does.)</span>
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106
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100
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="plaintext"></span>
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107
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101
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<pre style="margin: 0;"> <span id="LC101" class="line" lang="plaintext"></span>
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108
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<pre style="margin: 0;">-<span id="LC108" class="line" lang="plaintext">What does it mean that some older Bowtie 2 versions are “beta”?</span>
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109
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<pre style="margin: 0;">-<span id="LC109" class="line" lang="plaintext"></span>
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110
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<pre style="margin: 0;">-<span id="LC110" class="line" lang="plaintext">We said those Bowtie 2 versions were in “beta” to convey that it was not</span>
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111
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<pre style="margin: 0;">-<span id="LC111" class="line" lang="plaintext">as polished as a tool that had been around for a while, and was still in</span>
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112
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<pre style="margin: 0;">-<span id="LC112" class="line" lang="plaintext">flux. Since version 2.0.1, we declared Bowtie 2 was no longer “beta”.</span>
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113
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102
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<pre style="margin: 0;"> <span id="LC102" class="line" lang="plaintext"></span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="plaintext">OBTAINING BOWTIE 2</span>
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114
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104
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<pre style="margin: 0;"> <span id="LC104" class="line" lang="plaintext"></span>
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115
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105
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<pre style="margin: 0;"> <span id="LC105" class="line" lang="plaintext"></span>
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116
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<pre style="margin: 0;">-<span id="LC116" class="line" lang="plaintext">OBTAINING BOWTIE 2</span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="plaintext">Bowtie 2 is available from various package managers, notably Bioconda.</span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="plaintext">With Bioconda installed, you should be able to install Bowtie 2 with</span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="plaintext">conda install bowtie2.</span>
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117
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109
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<pre style="margin: 0;"> <span id="LC109" class="line" lang="plaintext"></span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="plaintext">Containerized versions of Bowtie 2 are also available via the</span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="plaintext">Biocontainers project (e.g. via Docker Hub).</span>
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118
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112
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<pre style="margin: 0;"> <span id="LC112" class="line" lang="plaintext"></span>
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119
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<pre style="margin: 0;">-<span id="LC119" class="line" lang="plaintext"><span class="idiff left right">Download Bowtie 2 sources and binaries from the Download section of the</span></span>
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120
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<pre style="margin: 0;">-<span id="LC120" class="line" lang="plaintext"><span class="idiff left right">Sourceforge site. Binaries are available for the Intel</span> x86_64</span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="plaintext"><span class="idiff left right">You can also download Bowtie 2 sources and binaries from the Download</span></span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="plaintext"><span class="idiff left right">section of the Sourceforge site. Binaries are available for the</span> x86_64</span>
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121
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115
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<pre style="margin: 0;"> <span id="LC115" class="line" lang="plaintext">architecture running Linux, Mac OS X, and Windows. If you plan to</span>
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122
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116
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<pre style="margin: 0;"> <span id="LC116" class="line" lang="plaintext">compile Bowtie 2 yourself, make sure to get the source package, i.e.,</span>
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117
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<pre style="margin: 0;"> <span id="LC117" class="line" lang="plaintext">the filename that ends in “-source.zip”.</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">@@ -145,8 +139,64 @@ Bowtie 2 can be run on many threads. By default, Bowtie 2 uses the</td>
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145
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139
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<pre style="margin: 0;"> <span id="LC139" class="line" lang="plaintext">Threading Building Blocks library (TBB) for this. If TBB is not</span>
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146
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140
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<pre style="margin: 0;"> <span id="LC140" class="line" lang="plaintext">available on your system (e.g. make prints an error like</span>
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147
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141
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<pre style="margin: 0;"> <span id="LC141" class="line" lang="plaintext">tbb/mutex.h: No such file or directory), you can install it yourself</span>
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148
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<pre style="margin: 0;">-<span id="LC148" class="line" lang="plaintext">(see Threading Building Blocks library) or build Bowtie 2 with</span>
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149
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<pre style="margin: 0;">-<span id="LC149" class="line" lang="plaintext">make NO_TBB=1 to use pthreads or Windows native multithreading instead.</span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="plaintext">from source (see Threading Building Blocks library) or install it using</span>
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143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="plaintext">your operating system’s preferred package manager. The table below list</span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="plaintext">some of the commands for a few of the more popular operating systems.</span>
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145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="plaintext"></span>
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146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="plaintext">OS</span>
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147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="plaintext">Sync Package List</span>
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148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="plaintext">Search</span>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="plaintext">Install</span>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="plaintext">Ubuntu, Mint, Debian</span>
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151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="plaintext"> apt-get update</span>
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152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="plaintext"></span>
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153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="plaintext"> apt-cache search tbb</span>
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154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="plaintext"></span>
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="plaintext"> apt-get install libtbb-dev</span>
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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="plaintext"></span>
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157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="plaintext">Fedora, CentOS</span>
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158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="plaintext"> yum check-update</span>
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159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="plaintext"></span>
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160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="plaintext">yum search tbb</span>
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161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="plaintext"></span>
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162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="plaintext"> yum install tbb-devel.x86_64</span>
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163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="plaintext"></span>
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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="plaintext">Arch</span>
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165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="plaintext"> packman -Sy</span>
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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="plaintext"></span>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="plaintext"> pacman -Ss tbb</span>
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168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="plaintext"></span>
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="plaintext"> pacman -S extra/intel-tbb</span>
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170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="plaintext"></span>
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171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="plaintext">Gentoo</span>
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172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="plaintext"> emerge --sync</span>
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173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="plaintext"></span>
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174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="plaintext"> emerge --search tbb</span>
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175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="plaintext"></span>
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176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="plaintext"> emerge dev-cpp/tbb</span>
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177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="plaintext"></span>
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178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="plaintext">MacOS</span>
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179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="plaintext"> brew update</span>
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180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="plaintext"></span>
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181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="plaintext"> brew search tbb</span>
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182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="plaintext"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="183" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="plaintext"> brew install tbb</span>
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184
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="plaintext"></span>
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<td class="diff-line-num new new_line" data-linenumber="185" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="plaintext">FreeBSD</span>
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<td class="diff-line-num new new_line" data-linenumber="186" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="plaintext"> portsnap fetch update</span>
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187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="plaintext"></span>
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188
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="plaintext"> make search name=tbb</span>
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189
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="plaintext"></span>
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190
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="plaintext"> cd /usr/ports/devel/tbb && make install && make clean</span>
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191
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="plaintext"></span>
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192
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="plaintext">The Bowtie 2 Makefile also includes recipes for basic automatic</span>
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193
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="plaintext">dependency management. Running make static-libs && make STATIC_BUILD=1</span>
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194
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="plaintext">will issue a series of commands that will: 1. download TBB and zlib 2.</span>
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195
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="plaintext">compile them as static libraries 3. link the resulting libraries to the</span>
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196
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="plaintext">compiled Bowtie 2 binaries</span>
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197
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="plaintext"></span>
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198
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="plaintext">If all fails Bowtie 2 can be built with make NO_TBB=1 to use pthreads or</span>
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199
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="plaintext">Windows native multithreading instead.</span>
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150
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200
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<pre style="margin: 0;"> <span id="LC200" class="line" lang="plaintext"></span>
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151
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201
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<pre style="margin: 0;"> <span id="LC201" class="line" lang="plaintext"></span>
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152
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202
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<pre style="margin: 0;"> <span id="LC202" class="line" lang="plaintext">Adding to PATH</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="923" style="width: 35px; color: rgba(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="973" style="width: 35px; color: rgba(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">@@ -923,6 +973,13 @@ Trim <int> bases from 5’ (left) end of each read before alignment</td>
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923
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973
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<pre style="margin: 0;"> <span id="LC973" class="line" lang="plaintext">Trim <int> bases from 3’ (right) end of each read before alignment</span>
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924
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974
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<pre style="margin: 0;"> <span id="LC974" class="line" lang="plaintext">(default: 0).</span>
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925
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975
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<pre style="margin: 0;"> <span id="LC975" class="line" lang="plaintext"></span>
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976
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<pre style="margin: 0;">+<span id="LC976" class="line" lang="plaintext"> --trim-to [3:|5:]<int></span>
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977
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<pre style="margin: 0;">+<span id="LC977" class="line" lang="plaintext"></span>
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978
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<pre style="margin: 0;">+<span id="LC978" class="line" lang="plaintext">Trim reads exceeding <int> bases. Bases will be trimmed from either the</span>
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979
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<pre style="margin: 0;">+<span id="LC979" class="line" lang="plaintext">3’ (right) or 5’ (left) end of the read. If the read end if not</span>
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980
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<pre style="margin: 0;">+<span id="LC980" class="line" lang="plaintext">specified, bowtie 2 will default to trimming from the 3’ (right) end of</span>
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981
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<pre style="margin: 0;">+<span id="LC981" class="line" lang="plaintext">the read. --trim-to and -3/-5 are mutually exclusive.</span>
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<pre style="margin: 0;">+<span id="LC982" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC983" class="line" lang="plaintext"> --phred33</span>
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984
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<pre style="margin: 0;"> <span id="LC984" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC985" class="line" lang="plaintext">Input qualities are ASCII chars equal to the Phred quality plus 33. This</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">@@ -1416,7 +1473,8 @@ print an asterisk in those fields instead.</td>
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1473
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<pre style="margin: 0;"> <span id="LC1473" class="line" lang="plaintext"></span>
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1417
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1474
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<pre style="margin: 0;"> <span id="LC1474" class="line" lang="plaintext"> --soft-clipped-unmapped-tlen</span>
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1418
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1475
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<pre style="margin: 0;"> <span id="LC1475" class="line" lang="plaintext"></span>
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1419
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<pre style="margin: 0;">-<span id="LC1419" class="line" lang="plaintext">Consider soft-clipped bases unmapped when calculating TLEN.</span>
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1476
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<pre style="margin: 0;">+<span id="LC1476" class="line" lang="plaintext">Consider soft-clipped bases unmapped when calculating TLEN. Only</span>
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1477
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<pre style="margin: 0;">+<span id="LC1477" class="line" lang="plaintext">available in --local mode.</span>
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1420
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1478
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<pre style="margin: 0;"> <span id="LC1478" class="line" lang="plaintext"></span>
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1479
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<pre style="margin: 0;"> <span id="LC1479" class="line" lang="plaintext"> --sam-no-qname-trunc</span>
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<pre style="margin: 0;"> <span id="LC1480" class="line" lang="plaintext"></span>
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<a href="https://salsa.debian.org/med-team/bowtie2/commit/157dbc209f47672a9a7167d16e3a324803906000#465370da702349b6dcb3f9f2026872cad6877efa"><strong>MANUAL.markdown</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">@@ -4,25 +4,18 @@</td>
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="markdown"> ! of this text document, or see the HTML manual online.</span>
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="markdown"> ! --></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="markdown"><span class="p">---</span></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="markdown"><span class="gh" style="color: #999;">title: Bowtie 2 Manual</span></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="markdown"><span class="gh" style="color: #999;">---</span></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="markdown"></span>
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7
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">Introduction</span></span>
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8
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">============</span></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="markdown"><span class="gh" style="color: #999;">What is Bowtie 2?</span></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="markdown"><span class="gh" style="color: #999;">-----------------</span></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: teal;">Bowtie 2</span><span class="p">]</span> is an ultrafast and memory-efficient tool for aligning sequencing</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="markdown">reads to long reference sequences. It is particularly good at aligning reads of</span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="markdown">about 50 up to 100s o<span class="idiff left right">r 1,000s o</span>f characters to relatively long (e.g. mammalian)</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="markdown">about 50 up to 100s of characters to relatively long (e.g. mammalian)</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="markdown">genomes. Bowtie 2 indexes the genome with an <span class="p">[</span><span class="nv" style="color: teal;">FM Index</span><span class="p">][</span><span class="ss" style="color: #990073;">FM Index Wiki</span><span class="p">]</span> (based on the</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: teal;">Burrows-Wheeler Transform</span><span class="p">]</span> or <span class="p">[</span><span class="nv" style="color: teal;">BWT</span><span class="p">]</span>) to keep its memory footprint small: for</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="markdown">the human genome, its memory footprint is typically around 3.2 gigabytes of RAM.</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="markdown"> Bowtie 2 supports gapped, local, and paired-end alignment modes. Multiple</span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="markdown">processors can be used simultaneously to achieve greater alignment speed.<span class="idiff left right"> </span></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="markdown"><span class="p"><span class="idiff left">[</span></span><span class="ss" style="color: #990073;"><span class="idiff">Cufflinks][</span></span><span class="p"><span class="idiff">]:</span></span><span class="idiff"> </span><span class="sx" style="color: #d14;"><span class="idiff">a</span></span><span class="idiff right"> tool for transcriptome assembly and isoform quantitiation from</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="markdown">processors can be used simultaneously to achieve greater alignment speed.</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="markdown">Bowtie 2 outputs alignments in <span class="p">[</span><span class="nv" style="color: teal;">SAM</span><span class="p">]</span> format, enabling interoperation with a</span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="markdown">large number of other tools (e.g. <span class="p">[</span><span class="nv" style="color: teal;">SAMtools</span><span class="p">]</span>, <span class="p">[</span><span class="nv" style="color: teal;">GATK</span><span class="p">]</span>) that use SAM. Bowtie 2 is</span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="markdown">distributed under the <span class="p">[</span><span class="nv" style="color: teal;">GPLv3 license</span><span class="p">]</span>, and it runs on the command line under</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">@@ -30,14 +23,18 @@ Windows, Mac OS X and Linux.</td>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: teal;">Bowtie 2</span><span class="p">]</span> is often the first step in pipelines for comparative genomics,</span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="markdown">including for variation calling, ChIP-seq, RNA-seq, BS-seq. <span class="p">[</span><span class="nv" style="color: teal;">Bowtie 2</span><span class="p">]</span> and</span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: teal;">Bowtie</span><span class="p">]</span> <span class="p">(</span><span class="sx" style="color: #d14;">also</span> called "<span class="p">[</span><span class="nv" style="color: teal;">Bowtie 1</span><span class="p">]</span>" here) are also tightly integrated into <span class="idiff left right">some</span></span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="markdown"><span class="idiff left">tools, including </span><span class="p"><span class="idiff">[</span></span><span class="nv" style="color: teal;"><span class="idiff">TopHat</span></span><span class="p"><span class="idiff">]</span></span><span class="idiff right">: a fast splice junction mapper for RNA-seq reads,</span></span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="markdown"><span class="idiff left">RNA-seq reads, </span><span class="p"><span class="idiff">[</span></span><span class="nv" style="color: teal;"><span class="idiff">Crossbow</span></span><span class="p"><span class="idiff">]</span></span><span class="idiff right">: a cloud-enabled software tool for analyzing</span></span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="markdown"><span class="idiff left">resequencing data, and </span><span class="p"><span class="idiff">[</span></span><span class="nv" style="color: teal;"><span class="idiff">Myrna</span></span><span class="p"><span class="idiff">]</span></span><span class="idiff right">: a cloud-enabled software tool for aligning</span></span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="markdown"><span class="idiff left right">RNA-seq reads and measuring differential gene expression.</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: teal;">Bowtie</span><span class="p">]</span> <span class="p">(</span><span class="sx" style="color: #d14;">also</span> called "<span class="p">[</span><span class="nv" style="color: teal;">Bowtie 1</span><span class="p">]</span>" here) are also tightly integrated into <span class="idiff left right">many</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="markdown"><span class="idiff left">other tools, some of which </span><span class="p"><span class="idiff">[</span></span><span class="nv" style="color: teal;"><span class="idiff">are listed here</span></span><span class="p"><span class="idiff">](</span></span><span class="sx" style="color: #d14;"><span class="idiff">http://bowtie-bio.sourceforge.net/bowtie2/other_tools.shtml</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff right">.</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="markdown"><span class="idiff left">If you use </span><span class="p"><span class="idiff">[</span></span><span class="nv" style="color: teal;"><span class="idiff">Bowtie 2</span></span><span class="p"><span class="idiff">]</span></span><span class="idiff right"> for your published research, please cite our work. Papers</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="markdown"><span class="idiff left right">describing Bowtie 2 are:</span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="markdown">If you use <span class="p">[</span><span class="nv" style="color: teal;">Bowtie 2</span><span class="p">]</span> for your published research, please cite the <span class="err" style="color: #a61717; background-color: #e3d2d2;">[</span>Bowtie</span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="markdown">paper]. Thank you!</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="markdown"><span class="p">*</span> Langmead B, Wilks C, Antonescu V, Charles R. <span class="err" style="color: #a61717; background-color: #e3d2d2;">[</span>Scaling read aligners to hundreds</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="markdown">of threads on general-purpose processors](https://doi.org/10.1093/bioinformatics/bty648). _Bioinformatics_. 2018 Jul 18. doi:</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="markdown"><span class="p">10.</span>1093/bioinformatics/bty648.</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="markdown"><span class="p">*</span> Langmead B, Salzberg SL. <span class="p">[</span><span class="nv" style="color: teal;">Fast gapped-read alignment with Bowtie 2</span><span class="p">](</span><span class="sx" style="color: #d14;">https://www.nature.com/articles/nmeth.1923</span><span class="p">)</span>. _Nature</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="markdown">Methods_. 2012 Mar 4;9(4):357-9. doi: 10.1038/nmeth.1923.</span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="markdown"><span class="gh" style="color: #999;">How is Bowtie 2 different from Bowtie 1?</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">@@ -91,35 +88,27 @@ arguments and genome index format are both different from Bowtie 1's.</td>
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="markdown"><span class="gh" style="color: #999;">What isn't Bowtie 2?</span></span>
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<pre style="margin: 0;"> <span id="LC89" class="line" lang="markdown"><span class="gh" style="color: #999;">--------------------</span></span>
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC94" class="line" lang="markdown">Bowtie 1 and Bowtie 2 are not general-purpose alignment tools like <span class="p">[</span><span class="nv" style="color: teal;">MUMmer</span><span class="p">]</span>,</span>
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<pre style="margin: 0;">-<span id="LC95" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: teal;">BLAST</span><span class="p">]</span> or <span class="p">[</span><span class="nv" style="color: teal;">Vmatch</span><span class="p">]</span>. Bowtie 2 works best when aligning to large genomes, though</span>
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<pre style="margin: 0;">-<span id="LC96" class="line" lang="markdown">it supports arbitrarily small reference sequences (e.g. amplicons). It handles</span>
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<pre style="margin: 0;">-<span id="LC97" class="line" lang="markdown">very long reads (i.e. upwards of 10s or 100s of kilobases), but it is optimized</span>
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<pre style="margin: 0;">-<span id="LC98" class="line" lang="markdown">for the read lengths and error modes yielded by recent sequencers, such as the</span>
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<pre style="margin: 0;">-<span id="LC99" class="line" lang="markdown">Illumina HiSeq 2000, Roche 454, and Ion Torrent instruments.</span>
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<pre style="margin: 0;">-<span id="LC100" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC101" class="line" lang="markdown">If your goal is to align two very large sequences (e.g. two genomes), consider</span>
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<pre style="margin: 0;">-<span id="LC102" class="line" lang="markdown">using <span class="p">[</span><span class="nv" style="color: teal;">MUMmer</span><span class="p">]</span>. If your goal is very sensitive alignment to a relatively short</span>
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<pre style="margin: 0;">-<span id="LC103" class="line" lang="markdown">reference sequence (e.g. a bacterial genome), this can be done with Bowtie 2 but</span>
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<pre style="margin: 0;">-<span id="LC104" class="line" lang="markdown">you may want to consider using tools like <span class="p">[</span><span class="nv" style="color: teal;">NUCmer</span><span class="p">]</span>, <span class="p">[</span><span class="nv" style="color: teal;">BLAT</span><span class="p">]</span>, or <span class="p">[</span><span class="nv" style="color: teal;">BLAST</span><span class="p">]</span>. These</span>
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<pre style="margin: 0;">-<span id="LC105" class="line" lang="markdown">tools can be extremely slow when the reference genome is long, but are often</span>
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<pre style="margin: 0;">-<span id="LC106" class="line" lang="markdown">adequate when the reference is short.</span>
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<pre style="margin: 0;">-<span id="LC107" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC108" class="line" lang="markdown">Bowtie 2 does not support alignment of colorspace reads.</span>
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<pre style="margin: 0;">-<span id="LC109" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="markdown">Bowtie 2 is geared toward aligning relatively short sequencing reads to long</span>
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="markdown">genomes. That said, it handles arbitrarily small reference sequences (e.g.</span>
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="markdown">amplicons) and very long reads (i.e. upwards of 10s or 100s of kilobases),</span>
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="markdown">though it is slower in those settings. It is optimized for the read lengths</span>
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="markdown">and error modes yielded by typical Illumina sequencers.</span>
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<pre style="margin: 0;"> <span id="LC96" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC111" class="line" lang="markdown"><span class="gh" style="color: #999;">What does it mean that some older Bowtie 2 versions are "beta"?</span></span>
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<pre style="margin: 0;">-<span id="LC112" class="line" lang="markdown"><span class="gh" style="color: #999;">--------------------------------------------------------------</span></span>
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="markdown">Bowtie 2 does not support alignment of colorspace reads. (Bowtie 1 does.)</span>
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<pre style="margin: 0;"> <span id="LC98" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC114" class="line" lang="markdown">We said those Bowtie 2 versions were in "beta" to convey that it was not as</span>
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<pre style="margin: 0;">-<span id="LC115" class="line" lang="markdown">polished as a tool that had been around for a while, and was still in flux.</span>
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<pre style="margin: 0;">-<span id="LC116" class="line" lang="markdown">Since version 2.0.1, we declared Bowtie 2 was no longer "beta".</span>
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">Obtaining Bowtie 2</span></span>
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<pre style="margin: 0;"> <span id="LC101" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">==================</span></span>
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<pre style="margin: 0;"> <span id="LC102" class="line" lang="markdown"></span>
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121
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<pre style="margin: 0;">-<span id="LC121" class="line" lang="markdown">Download Bowtie 2 sources and binaries from the <span class="p">[</span><span class="nv" style="color: teal;">Download</span><span class="p">]</span> section of the</span>
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122
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<pre style="margin: 0;">-<span id="LC122" class="line" lang="markdown">Sourceforge site. Binaries are available for the Intel <span class="sb" style="color: #d14;">`x86_64`</span> architecture</span>
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="markdown">Bowtie 2 is available from various package managers, notably <span class="p">[</span><span class="nv" style="color: teal;">Bioconda</span><span class="p">](</span><span class="sx" style="color: #d14;">https://anaconda.org/bioconda/bowtie2</span><span class="p">)</span>.</span>
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="markdown">With Bioconda installed, you should be able to install Bowtie 2 with <span class="sb" style="color: #d14;">`conda</span></span>
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="markdown"><span class="sb" style="color: #d14;">install bowtie2`</span>.</span>
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="markdown">Containerized versions of Bowtie 2 are also available via the <span class="p">[</span><span class="nv" style="color: teal;">Biocontainers</span><span class="p">](</span><span class="sx" style="color: #d14;">https://BioContainers.pro</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="markdown">project (e.g. <span class="p">[</span><span class="nv" style="color: teal;">via Docker Hub</span><span class="p">](</span><span class="sx" style="color: #d14;">https://hub.docker.com/r/biocontainers/bowtie2/</span><span class="p">)</span>).</span>
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="markdown">You can also download Bowtie 2 sources and binaries from the <span class="p">[</span><span class="nv" style="color: teal;">Download</span><span class="p">]</span> section</span>
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="markdown">of the Sourceforge site. Binaries are available for the <span class="sb" style="color: #d14;">`x86_64`</span> architecture</span>
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<pre style="margin: 0;"> <span id="LC112" class="line" lang="markdown">running Linux, Mac OS X, and Windows. If you plan to compile Bowtie 2 yourself,</span>
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<pre style="margin: 0;"> <span id="LC113" class="line" lang="markdown">make sure to get the source package, i.e., the filename that ends in</span>
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<pre style="margin: 0;"> <span id="LC114" class="line" lang="markdown">"-source.zip".</span>
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<td class="diff-line-num unfold js-unfold old_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="diff-line-num unfold js-unfold new_line" data-linenumber="134" style="width: 35px; color: rgba(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">@@ -145,9 +134,118 @@ from the MSYS environment.</td>
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<pre style="margin: 0;"> <span id="LC134" class="line" lang="markdown">Bowtie 2 can be run on many threads. By default, Bowtie 2 uses the Threading</span>
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<pre style="margin: 0;"> <span id="LC135" class="line" lang="markdown">Building Blocks library (TBB) for this. If TBB is not available on your system</span>
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<pre style="margin: 0;"> <span id="LC136" class="line" lang="markdown">(e.g. <span class="sb" style="color: #d14;">`make`</span> prints an error like <span class="sb" style="color: #d14;">`tbb/mutex.h: No such file or directory`</span>),</span>
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<pre style="margin: 0;">-<span id="LC148" class="line" lang="markdown">you can install it yourself (see <span class="p">[</span><span class="nv" style="color: teal;">Threading Building Blocks library</span><span class="p">]</span>) or build</span>
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<pre style="margin: 0;">-<span id="LC149" class="line" lang="markdown">Bowtie 2 with <span class="sb" style="color: #d14;">`make NO_TBB=1`</span> to use pthreads or Windows native multithreading</span>
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<pre style="margin: 0;">-<span id="LC150" class="line" lang="markdown">instead.</span>
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="markdown">you can install it yourself from source (see <span class="p">[</span><span class="nv" style="color: teal;">Threading Building Blocks library</span><span class="p">]</span>)</span>
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="markdown">or install it using your operating system's preferred package manager.</span>
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="markdown">The table below list some of the commands for a few of the more popular</span>
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="markdown">operating systems.</span>
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="markdown"><span class="nt" style="color: navy;"><table></span></span>
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="markdown"><span class="nt" style="color: navy;"><tr><th></span>OS<span class="nt" style="color: navy;"></th><th></span>Sync Package List<span class="nt" style="color: navy;"></th><th></span>Search<span class="nt" style="color: navy;"></th><th></span>Install<span class="nt" style="color: navy;"></th></tr></span></span>
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="markdown"><span class="nt" style="color: navy;"><tr><td></span>Ubuntu, Mint, Debian<span class="nt" style="color: navy;"></td></span></span>
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="markdown"><span class="sb" style="color: #d14;"> apt-get update</span></span>
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="markdown"><span class="sb" style="color: #d14;"> apt-cache search tbb</span></span>
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157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="markdown"><span class="sb" style="color: #d14;"> apt-get install libtbb-dev</span></span>
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158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="markdown"></span>
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159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="markdown"><span class="nt" style="color: navy;"></td></tr></span></span>
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160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="markdown"><span class="nt" style="color: navy;"><tr><td></span>Fedora, CentOS<span class="nt" style="color: navy;"></td></span></span>
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161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="markdown"><span class="nt" style="color: navy;"><td></span></span>
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162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="markdown"></span>
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163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="markdown"><span class="sb" style="color: #d14;"> yum check-update</span></span>
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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="markdown"></span>
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165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="markdown"><span class="nt" style="color: navy;"></td></span></span>
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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="markdown"><span class="nt" style="color: navy;"><td></span></span>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="markdown"> yum search tbb</span>
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168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="markdown"></span>
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="markdown"><span class="nt" style="color: navy;"></td></span></span>
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170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="markdown"><span class="nt" style="color: navy;"><td></span></span>
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171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="markdown"></span>
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172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="markdown"><span class="sb" style="color: #d14;"> yum install tbb-devel.x86_64</span></span>
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173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="markdown"></span>
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174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="markdown"><span class="nt" style="color: navy;"></td></tr></span></span>
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175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="markdown"><span class="nt" style="color: navy;"><tr><td></span>Arch<span class="nt" style="color: navy;"></td></span></span>
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176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="markdown"><span class="nt" style="color: navy;"><td></span></span>
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177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="markdown"></span>
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178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="markdown"><span class="sb" style="color: #d14;"> packman -Sy</span></span>
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179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="markdown"></span>
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180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="markdown"><span class="nt" style="color: navy;"></td></span></span>
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181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="markdown"><span class="nt" style="color: navy;"><td></span></span>
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182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="markdown"></span>
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183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="markdown"><span class="sb" style="color: #d14;"> pacman -Ss tbb</span></span>
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184
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="markdown"></span>
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185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="markdown"><span class="nt" style="color: navy;"></td></span></span>
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186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="markdown"><span class="nt" style="color: navy;"><td></span></span>
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187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="markdown"></span>
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188
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="markdown"><span class="sb" style="color: #d14;"> pacman -S extra/intel-tbb</span></span>
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189
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="markdown"></span>
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190
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="markdown"><span class="nt" style="color: navy;"></td></tr></span></span>
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191
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="markdown"><span class="nt" style="color: navy;"><tr><td></span>Gentoo<span class="nt" style="color: navy;"></td></span></span>
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192
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="markdown"><span class="nt" style="color: navy;"><td></span></span>
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193
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="markdown"></span>
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194
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="markdown"><span class="sb" style="color: #d14;"> emerge --sync</span></span>
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195
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="markdown"></span>
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196
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="markdown"><span class="nt" style="color: navy;"></td></span></span>
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197
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="markdown"><span class="nt" style="color: navy;"><td></span></span>
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198
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="markdown"></span>
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199
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="markdown"><span class="sb" style="color: #d14;"> emerge --search tbb</span></span>
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200
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="markdown"></span>
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201
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="markdown"><span class="nt" style="color: navy;"></td></span></span>
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202
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="markdown"><span class="nt" style="color: navy;"><td></span></span>
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203
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="markdown"></span>
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204
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="markdown"><span class="sb" style="color: #d14;"> emerge dev-cpp/tbb</span></span>
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205
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="markdown"></span>
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206
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="markdown"><span class="nt" style="color: navy;"></td></span></span>
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207
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="markdown"><span class="nt" style="color: navy;"><tr><td></span>MacOS<span class="nt" style="color: navy;"></td></span></span>
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208
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="markdown"><span class="nt" style="color: navy;"><td></span></span>
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209
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="markdown"></span>
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210
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="markdown"><span class="sb" style="color: #d14;"> brew update</span></span>
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211
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="markdown"></span>
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212
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="markdown"><span class="nt" style="color: navy;"></td></span></span>
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213
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="markdown"><span class="nt" style="color: navy;"><td></span></span>
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214
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="markdown"></span>
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215
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="markdown"><span class="sb" style="color: #d14;"> brew search tbb</span></span>
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216
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="markdown"></span>
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217
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218
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="markdown"><span class="nt" style="color: navy;"><td></span></span>
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219
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="markdown"></span>
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220
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="markdown"><span class="sb" style="color: #d14;"> brew install tbb</span></span>
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221
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="markdown"></span>
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222
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="markdown"><span class="nt" style="color: navy;"></td></tr></span></span>
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223
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="markdown"><span class="nt" style="color: navy;"><tr><td></span>FreeBSD<span class="nt" style="color: navy;"></td></span></span>
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224
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="markdown"><span class="nt" style="color: navy;"><td></span></span>
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225
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="markdown"></span>
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226
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="markdown"><span class="sb" style="color: #d14;"> portsnap fetch update</span></span>
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227
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<pre style="margin: 0;">+<span id="LC227" class="line" lang="markdown"></span>
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228
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="markdown"><span class="nt" style="color: navy;"></td></span></span>
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229
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="markdown"><span class="nt" style="color: navy;"><td></span></span>
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230
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<pre style="margin: 0;">+<span id="LC230" class="line" lang="markdown"></span>
</pre>
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231
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<pre style="margin: 0;">+<span id="LC231" class="line" lang="markdown"><span class="sb" style="color: #d14;"> make search name=tbb</span></span>
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232
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<pre style="margin: 0;">+<span id="LC232" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC236" class="line" lang="markdown"><span class="sb" style="color: #d14;"> cd /usr/ports/devel/tbb && make install && make clean</span></span>
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="markdown"><span class="nt" style="color: navy;"></table></span></span>
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<pre style="margin: 0;">+<span id="LC239" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC240" class="line" lang="markdown">The Bowtie 2 Makefile also includes recipes for basic automatic dependency</span>
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<pre style="margin: 0;">+<span id="LC241" class="line" lang="markdown">management. Running <span class="sb" style="color: #d14;">`make static-libs && make STATIC_BUILD=1`</span> will issue</span>
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<pre style="margin: 0;">+<span id="LC242" class="line" lang="markdown">a series of commands that will:</span>
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<pre style="margin: 0;">+<span id="LC243" class="line" lang="markdown"><span class="p"> 1.</span> download TBB and zlib</span>
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<pre style="margin: 0;">+<span id="LC244" class="line" lang="markdown"><span class="p"> 2.</span> compile them as static libraries</span>
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<pre style="margin: 0;">+<span id="LC245" class="line" lang="markdown"><span class="p"> 3.</span> link the resulting libraries to the compiled Bowtie 2 binaries</span>
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<pre style="margin: 0;">+<span id="LC246" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="markdown">If all fails Bowtie 2 can be built with <span class="sb" style="color: #d14;">`make NO_TBB=1`</span> to use pthreads</span>
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<pre style="margin: 0;">+<span id="LC248" class="line" lang="markdown">or Windows native multithreading instead.</span>
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<pre style="margin: 0;"> <span id="LC249" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC250" class="line" lang="markdown"><span class="gh" style="color: #999;">Adding to PATH</span></span>
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<pre style="margin: 0;"> <span id="LC251" class="line" lang="markdown"><span class="gh" style="color: #999;">--------------</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">@@ -211,7 +309,7 @@ end-to-end mode or in local mode.</td>
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<pre style="margin: 0;"> <span id="LC309" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC310" class="line" lang="markdown"><span class="sb" style="color: #d14;"> Read: GACTGGGCGATCTCGACTTCG</span></span>
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<pre style="margin: 0;"> <span id="LC311" class="line" lang="markdown"><span class="sb" style="color: #d14;"> Reference: GACTGCGATCTCGACATCG</span></span>
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<pre style="margin: 0;">-<span id="LC214" class="line" lang="markdown"><span class="sb" style="color: #d14;"><span class="idiff left right"> </span></span></span>
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<pre style="margin: 0;">+<span id="LC312" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC313" class="line" lang="markdown"><span class="sb" style="color: #d14;"> Alignment:</span></span>
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216
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314
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<pre style="margin: 0;"> <span id="LC314" class="line" lang="markdown"><span class="sb" style="color: #d14;"> Read: GACTGGGCGATCTCGACTTCG</span></span>
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217
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315
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<pre style="margin: 0;"> <span id="LC315" class="line" lang="markdown"><span class="sb" style="color: #d14;"> ||||| |||||||||| |||</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="325" style="width: 35px; color: rgba(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">@@ -227,7 +325,7 @@ in local mode.</td>
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227
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325
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<pre style="margin: 0;"> <span id="LC325" class="line" lang="markdown"></span>
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228
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326
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<pre style="margin: 0;"> <span id="LC326" class="line" lang="markdown"><span class="sb" style="color: #d14;"> Read: ACGGTTGCGTTAATCCGCCACG</span></span>
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229
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327
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<pre style="margin: 0;"> <span id="LC327" class="line" lang="markdown"><span class="sb" style="color: #d14;"> Reference: TAACTTGCGTTAAATCCGCCTGG</span></span>
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230
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<pre style="margin: 0;">-<span id="LC230" class="line" lang="markdown"><span class="sb" style="color: #d14;"><span class="idiff left right"> </span></span></span>
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328
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<pre style="margin: 0;">+<span id="LC328" class="line" lang="markdown"></span>
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231
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329
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<pre style="margin: 0;"> <span id="LC329" class="line" lang="markdown"><span class="sb" style="color: #d14;"> Alignment:</span></span>
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232
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330
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<pre style="margin: 0;"> <span id="LC330" class="line" lang="markdown"><span class="sb" style="color: #d14;"> Read: ACGGTTGCGTTAA-TCCGCCACG</span></span>
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233
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331
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<pre style="margin: 0;"> <span id="LC331" class="line" lang="markdown"><span class="sb" style="color: #d14;"> ||||||||| ||||||</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 +563,7 @@ alignment mode.</td>
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563
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<pre style="margin: 0;"> <span id="LC563" class="line" lang="markdown"></span>
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466
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<pre style="margin: 0;"> <span id="LC564" class="line" lang="markdown">In general, when we say that a read has an alignment, we mean that it has a</span>
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467
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<pre style="margin: 0;"> <span id="LC565" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: teal;">valid alignment</span><span class="p">]</span>. When we say that a read has multiple alignments, we mean</span>
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<pre style="margin: 0;">-<span id="LC468" class="line" lang="markdown">that it has multiple alignments that are valid and distinct from one another.<span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC566" class="line" lang="markdown">that it has multiple alignments that are valid and distinct from one another.</span>
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567
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<pre style="margin: 0;"> <span id="LC567" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC568" class="line" lang="markdown"></span>
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569
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<pre style="margin: 0;"> <span id="LC569" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Distinct alignments map a read to different places</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="663" style="width: 35px; color: rgba(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="761" style="width: 35px; color: rgba(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">@@ -663,7 +761,7 @@ reflect only one of those reasons.</td>
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663
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761
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<pre style="margin: 0;"> <span id="LC761" class="line" lang="markdown"><span class="gh" style="color: #999;">Alignment summary</span></span>
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664
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762
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<pre style="margin: 0;"> <span id="LC762" class="line" lang="markdown"><span class="gh" style="color: #999;">------------------</span></span>
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<pre style="margin: 0;"> <span id="LC763" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC666" class="line" lang="markdown">When Bowtie 2 finishes running, it prints messages summarizing what happened.<span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC764" class="line" lang="markdown">When Bowtie 2 finishes running, it prints messages summarizing what happened.</span>
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765
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<pre style="margin: 0;"> <span id="LC765" class="line" lang="markdown">These messages are printed to the "standard error" ("stderr") filehandle. For</span>
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668
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766
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<pre style="margin: 0;"> <span id="LC766" class="line" lang="markdown">datasets consisting of unpaired reads, the summary might look like this:</span>
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767
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<pre style="margin: 0;"> <span id="LC767" class="line" lang="markdown"></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="795" style="width: 35px; color: rgba(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">@@ -697,7 +795,7 @@ The indentation indicates how subtotals relate to totals.</td>
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697
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795
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<pre style="margin: 0;"> <span id="LC795" class="line" lang="markdown"><span class="gh" style="color: #999;">Wrapper scripts</span></span>
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698
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796
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<pre style="margin: 0;"> <span id="LC796" class="line" lang="markdown"><span class="gh" style="color: #999;">---------------</span></span>
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699
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797
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<pre style="margin: 0;"> <span id="LC797" class="line" lang="markdown"></span>
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700
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<pre style="margin: 0;">-<span id="LC700" class="line" lang="markdown">The <span class="sb" style="color: #d14;">`bowtie2`</span>, <span class="sb" style="color: #d14;">`bowtie2-build`</span> and <span class="sb" style="color: #d14;">`bowtie2-inspect`</span> executables are actually<span class="idiff left right"> </span></span>
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798
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<pre style="margin: 0;">+<span id="LC798" class="line" lang="markdown">The <span class="sb" style="color: #d14;">`bowtie2`</span>, <span class="sb" style="color: #d14;">`bowtie2-build`</span> and <span class="sb" style="color: #d14;">`bowtie2-inspect`</span> executables are actually</span>
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701
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799
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<pre style="margin: 0;"> <span id="LC799" class="line" lang="markdown">wrapper scripts that call binary programs as appropriate. The wrappers shield</span>
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702
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800
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<pre style="margin: 0;"> <span id="LC800" class="line" lang="markdown">users from having to distinguish between "small" and "large" index formats,</span>
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801
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<pre style="margin: 0;"> <span id="LC801" class="line" lang="markdown">discussed briefly in the following section. Also, the <span class="sb" style="color: #d14;">`bowtie2`</span> wrapper</span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1083" style="width: 35px; color: rgba(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">@@ -985,6 +1083,17 @@ Trim `<int>` bases from 5' (left) end of each read before alignment (default: 0)</td>
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985
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1083
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<pre style="margin: 0;"> <span id="LC1083" class="line" lang="markdown"></span>
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986
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1084
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<pre style="margin: 0;"> <span id="LC1084" class="line" lang="markdown">Trim <span class="sb" style="color: #d14;">`<int>`</span> bases from 3' (right) end of each read before alignment (default: 0).</span>
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987
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1085
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<pre style="margin: 0;"> <span id="LC1085" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC1086" class="line" lang="markdown"><span class="nt" style="color: navy;"></td></tr><tr><td</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"bowtie2-options-trim-to"</span><span class="nt" style="color: navy;">></span></span>
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1087
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<pre style="margin: 0;">+<span id="LC1087" class="line" lang="markdown"></span>
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1088
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<pre style="margin: 0;">+<span id="LC1088" class="line" lang="markdown"><span class="sb" style="color: #d14;"> --trim-to [3:|5:]<int></span></span>
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1089
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<pre style="margin: 0;">+<span id="LC1089" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC1090" class="line" lang="markdown"><span class="nt" style="color: navy;"></td><td></span></span>
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1091
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<pre style="margin: 0;">+<span id="LC1091" class="line" lang="markdown"></span>
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1092
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<pre style="margin: 0;">+<span id="LC1092" class="line" lang="markdown">Trim reads exceeding <span class="sb" style="color: #d14;">`<int>`</span> bases. Bases will be trimmed from either the 3' (right)</span>
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1093
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<pre style="margin: 0;">+<span id="LC1093" class="line" lang="markdown">or 5' (left) end of the read. If the read end if not specified, bowtie 2 will default</span>
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<pre style="margin: 0;">+<span id="LC1094" class="line" lang="markdown">to trimming from the 3' (right) end of the read. <span class="p">[</span><span class="nv" style="color: teal;">`--trim-to`</span><span class="p">]</span> and <span class="p">[</span><span class="nv" style="color: teal;">`-3`</span><span class="p">]</span>/<span class="p">[</span><span class="nv" style="color: teal;">`-5`</span><span class="p">]</span> are</span>
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<pre style="margin: 0;">+<span id="LC1095" class="line" lang="markdown">mutually exclusive.</span>
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<pre style="margin: 0;">+<span id="LC1096" class="line" lang="markdown"></span>
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1097
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<pre style="margin: 0;"> <span id="LC1097" class="line" lang="markdown"><span class="nt" style="color: navy;"></td></tr><tr><td</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"bowtie2-options-phred33-quals"</span><span class="nt" style="color: navy;">></span></span>
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1098
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<pre style="margin: 0;"> <span id="LC1098" class="line" lang="markdown"></span>
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1099
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<pre style="margin: 0;"> <span id="LC1099" class="line" lang="markdown"><span class="sb" style="color: #d14;"> --phred33</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1198" style="width: 35px; color: rgba(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="1307" style="width: 35px; color: rgba(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">@@ -1198,7 +1307,7 @@ gaps. Default: 15.</td>
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1198
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1307
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<pre style="margin: 0;"> <span id="LC1307" class="line" lang="markdown"></span>
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1199
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1308
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<pre style="margin: 0;"> <span id="LC1308" class="line" lang="markdown"><span class="nt" style="color: navy;"></td><td></span></span>
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1200
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1309
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<pre style="margin: 0;"> <span id="LC1309" class="line" lang="markdown"></span>
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1201
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<pre style="margin: 0;">-<span id="LC1201" class="line" lang="markdown">Disallow gaps within <span class="sb" style="color: #d14;">`<int>`</span> positions of the beginning or end of the read.<span class="idiff left right"> </span></span>
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1310
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<pre style="margin: 0;">+<span id="LC1310" class="line" lang="markdown">Disallow gaps within <span class="sb" style="color: #d14;">`<int>`</span> positions of the beginning or end of the read.</span>
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1202
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1311
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<pre style="margin: 0;"> <span id="LC1311" class="line" lang="markdown">Default: 4.</span>
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1203
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1312
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<pre style="margin: 0;"> <span id="LC1312" class="line" lang="markdown"></span>
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1204
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1313
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<pre style="margin: 0;"> <span id="LC1313" class="line" lang="markdown"><span class="nt" style="color: navy;"></td></tr></span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1209" style="width: 35px; color: rgba(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="1318" style="width: 35px; color: rgba(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">@@ -1209,7 +1318,7 @@ Default: 4.</td>
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1209
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1318
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<pre style="margin: 0;"> <span id="LC1318" class="line" lang="markdown"><span class="nt" style="color: navy;"></td><td></span></span>
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1210
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1319
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<pre style="margin: 0;"> <span id="LC1319" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC1320" class="line" lang="markdown">When calculating a mismatch penalty, always consider the quality value at the</span>
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1212
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<pre style="margin: 0;">-<span id="LC1212" class="line" lang="markdown">mismatched position to be the highest possible, regardless of the actual value.<span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC1321" class="line" lang="markdown">mismatched position to be the highest possible, regardless of the actual value.</span>
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1213
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<pre style="margin: 0;"> <span id="LC1322" class="line" lang="markdown">I.e. input is treated as though all quality values are high. This is also the</span>
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1214
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1323
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<pre style="margin: 0;"> <span id="LC1323" class="line" lang="markdown">default behavior when the input doesn't specify quality values (e.g. in <span class="p">[</span><span class="nv" style="color: teal;">`-f`</span><span class="p">]</span>,</span>
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1215
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1324
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<pre style="margin: 0;"> <span id="LC1324" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: teal;">`-r`</span><span class="p">]</span>, or <span class="p">[</span><span class="nv" style="color: teal;">`-c`</span><span class="p">]</span> modes).</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1227" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1336" style="width: 35px; color: rgba(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">@@ -1227,7 +1336,7 @@ not attempt to align unpaired reads against the reverse-complement (Crick)</td>
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1227
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<pre style="margin: 0;"> <span id="LC1336" class="line" lang="markdown">reference strand. In paired-end mode, <span class="sb" style="color: #d14;">`--nofw`</span> and <span class="sb" style="color: #d14;">`--norc`</span> pertain to the</span>
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1228
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<pre style="margin: 0;"> <span id="LC1337" class="line" lang="markdown">fragments; i.e. specifying <span class="sb" style="color: #d14;">`--nofw`</span> causes <span class="sb" style="color: #d14;">`bowtie2`</span> to explore only those</span>
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1229
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<pre style="margin: 0;"> <span id="LC1338" class="line" lang="markdown">paired-end configurations corresponding to fragments from the reverse-complement</span>
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1230
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<pre style="margin: 0;">-<span id="LC1230" class="line" lang="markdown">(Crick) strand. Default: both strands enabled.<span class="idiff left right"> </span></span>
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1339
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<pre style="margin: 0;">+<span id="LC1339" class="line" lang="markdown">(Crick) strand. Default: both strands enabled.</span>
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1340
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<pre style="margin: 0;"> <span id="LC1340" class="line" lang="markdown"></span>
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1232
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1341
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<pre style="margin: 0;"> <span id="LC1341" class="line" lang="markdown"><span class="nt" style="color: navy;"></td></tr></span></span>
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1233
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1342
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<pre style="margin: 0;"> <span id="LC1342" class="line" lang="markdown"><span class="nt" style="color: navy;"><tr><td</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"bowtie2-options-no-1mm-upfront"</span><span class="nt" style="color: navy;">></span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1382" style="width: 35px; color: rgba(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="1491" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1382,7 +1491,7 @@ alignment equals the sum of the alignment scores of the individual mates. Each</td>
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1382
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1491
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<pre style="margin: 0;"> <span id="LC1491" class="line" lang="markdown">reported read or pair alignment beyond the first has the SAM 'secondary' bit</span>
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1383
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<pre style="margin: 0;"> <span id="LC1492" class="line" lang="markdown">(which equals 256) set in its FLAGS field. For reads that have more than</span>
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<pre style="margin: 0;"> <span id="LC1493" class="line" lang="markdown"><span class="sb" style="color: #d14;">`<int>`</span> distinct, valid alignments, <span class="sb" style="color: #d14;">`bowtie2`</span> does not guarantee that the</span>
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1385
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<pre style="margin: 0;">-<span id="LC1385" class="line" lang="markdown"><span class="sb" style="color: #d14;">`<int>`</span> alignments reported are the best possible in terms of alignment score.<span class="idiff left right"> </span></span>
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1494
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<pre style="margin: 0;">+<span id="LC1494" class="line" lang="markdown"><span class="sb" style="color: #d14;">`<int>`</span> alignments reported are the best possible in terms of alignment score.</span>
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1386
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<pre style="margin: 0;"> <span id="LC1495" class="line" lang="markdown"><span class="sb" style="color: #d14;">`-k`</span> is mutually exclusive with <span class="p">[</span><span class="nv" style="color: teal;">`-a`</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="markdown"></span>
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<pre style="margin: 0;"> <span id="LC1497" class="line" lang="markdown">Note: Bowtie 2 is not designed with large values for <span class="sb" style="color: #d14;">`-k`</span> in mind, and when</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1459" style="width: 35px; color: rgba(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="1568" style="width: 35px; color: rgba(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">@@ -1459,7 +1568,7 @@ Bowtie 2 scan a larger window to determine if a concordant alignment exists.</td>
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<pre style="margin: 0;"> <span id="LC1568" class="line" lang="markdown">For typical fragment length ranges (200 to 400 nucleotides), Bowtie 2 is very</span>
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<pre style="margin: 0;"> <span id="LC1569" class="line" lang="markdown">efficient.</span>
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<pre style="margin: 0;"> <span id="LC1570" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC1462" class="line" lang="markdown">Default: 0 (essentially imposing no minimum)<span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC1571" class="line" lang="markdown">Default: 0 (essentially imposing no minimum)</span>
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1463
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1572
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<pre style="margin: 0;"> <span id="LC1572" class="line" lang="markdown"></span>
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1573
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<pre style="margin: 0;"> <span id="LC1573" class="line" lang="markdown"><span class="nt" style="color: navy;"></td></tr></span></span>
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1574
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<pre style="margin: 0;"> <span id="LC1574" class="line" lang="markdown"><span class="nt" style="color: navy;"><tr><td</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"bowtie2-options-X"</span><span class="nt" style="color: navy;">></span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1556" style="width: 35px; color: rgba(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="1665" style="width: 35px; color: rgba(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">@@ -1556,7 +1665,7 @@ can contain the other in a concordant alignment.</td>
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1556
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1665
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<pre style="margin: 0;"> <span id="LC1665" class="line" lang="markdown"><span class="nt" style="color: navy;"></td><td></span></span>
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1557
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1666
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<pre style="margin: 0;"> <span id="LC1666" class="line" lang="markdown"></span>
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1558
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1667
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<pre style="margin: 0;"> <span id="LC1667" class="line" lang="markdown">If one mate alignment overlaps the other at all, consider that to be</span>
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1559
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<td class="diff-line-num new_line old" data-linenumber="1668" 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="LC1559" class="line" lang="markdown">non-concordant. See also: <span class="p">[</span><span class="nv" style="color: teal;">Mates can overlap, contain or dovetail each other</span><span class="p">]</span>.<span class="idiff left right"> </span></span>
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1668
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<pre style="margin: 0;">+<span id="LC1668" class="line" lang="markdown">non-concordant. See also: <span class="p">[</span><span class="nv" style="color: teal;">Mates can overlap, contain or dovetail each other</span><span class="p">]</span>.</span>
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1560
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1669
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<pre style="margin: 0;"> <span id="LC1669" class="line" lang="markdown">Default: mates can overlap in a concordant alignment.</span>
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1561
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1670
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<pre style="margin: 0;"> <span id="LC1670" class="line" lang="markdown"></span>
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1671
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<pre style="margin: 0;"> <span id="LC1671" class="line" lang="markdown"><span class="nt" style="color: navy;"></td></tr></table></span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1571" style="width: 35px; color: rgba(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="1680" style="width: 35px; color: rgba(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">@@ -1571,7 +1680,7 @@ Default: mates can overlap in a concordant alignment.</td>
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1571
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1680
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<pre style="margin: 0;"> <span id="LC1680" class="line" lang="markdown"></span>
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1572
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1681
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<pre style="margin: 0;"> <span id="LC1681" class="line" lang="markdown"><span class="nt" style="color: navy;"></td><td></span></span>
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1573
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1682
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<pre style="margin: 0;"> <span id="LC1682" class="line" lang="markdown"></span>
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1574
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<pre style="margin: 0;">-<span id="LC1574" class="line" lang="markdown">Print the wall-clock time required to load the index files and align the reads.<span class="idiff left right"> </span></span>
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1683
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<pre style="margin: 0;">+<span id="LC1683" class="line" lang="markdown">Print the wall-clock time required to load the index files and align the reads.</span>
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1575
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1684
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<pre style="margin: 0;"> <span id="LC1684" class="line" lang="markdown">This is printed to the "standard error" ("stderr") filehandle. Default: off.</span>
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1576
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1685
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<pre style="margin: 0;"> <span id="LC1685" class="line" lang="markdown"></span>
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1577
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1686
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<pre style="margin: 0;"> <span id="LC1686" class="line" lang="markdown"><span class="nt" style="color: navy;"></td></tr></span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1587" style="width: 35px; color: rgba(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="1696" style="width: 35px; color: rgba(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">@@ -1587,10 +1696,10 @@ This is printed to the "standard error" ("stderr") filehandle. Default: off.</td>
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1587
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1696
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<pre style="margin: 0;"> <span id="LC1696" class="line" lang="markdown">Write unpaired reads that fail to align to file at <span class="sb" style="color: #d14;">`<path>`</span>. These reads</span>
</pre>
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1588
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1697
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<pre style="margin: 0;"> <span id="LC1697" class="line" lang="markdown">correspond to the SAM records with the FLAGS <span class="sb" style="color: #d14;">`0x4`</span> bit set and neither the</span>
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1589
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1698
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<pre style="margin: 0;"> <span id="LC1698" class="line" lang="markdown"><span class="sb" style="color: #d14;">`0x40`</span> nor <span class="sb" style="color: #d14;">`0x80`</span> bits set. If <span class="sb" style="color: #d14;">`--un-gz`</span> is specified, output will be gzip</span>
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1590
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<pre style="margin: 0;">-<span id="LC1590" class="line" lang="markdown">compressed. If <span class="sb" style="color: #d14;">`--un-bz2`</span> or <span class="sb" style="color: #d14;">`--un-lz4`</span> is specified, output will be bzip2 or<span class="idiff left right"> </span></span>
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1591
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<pre style="margin: 0;">-<span id="LC1591" class="line" lang="markdown">lz4 compressed. Reads written in this way will appear exactly as they did in<span class="idiff left right"> </span></span>
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<pre style="margin: 0;">-<span id="LC1592" class="line" lang="markdown">the input file, without any modification (same sequence, same name, same quality<span class="idiff left right"> </span></span>
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<pre style="margin: 0;">-<span id="LC1593" class="line" lang="markdown">string, same quality encoding). Reads will not necessarily appear in the same<span class="idiff left right"> </span></span>
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1699
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<pre style="margin: 0;">+<span id="LC1699" class="line" lang="markdown">compressed. If <span class="sb" style="color: #d14;">`--un-bz2`</span> or <span class="sb" style="color: #d14;">`--un-lz4`</span> is specified, output will be bzip2 or</span>
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1700
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<pre style="margin: 0;">+<span id="LC1700" class="line" lang="markdown">lz4 compressed. Reads written in this way will appear exactly as they did in</span>
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<pre style="margin: 0;">+<span id="LC1701" class="line" lang="markdown">the input file, without any modification (same sequence, same name, same quality</span>
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1702
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<pre style="margin: 0;">+<span id="LC1702" class="line" lang="markdown">string, same quality encoding). Reads will not necessarily appear in the same</span>
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1594
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1703
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<pre style="margin: 0;"> <span id="LC1703" class="line" lang="markdown">order as they did in the input.</span>
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1595
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1704
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<pre style="margin: 0;"> <span id="LC1704" class="line" lang="markdown"></span>
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1596
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1705
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<pre style="margin: 0;"> <span id="LC1705" class="line" lang="markdown"><span class="nt" style="color: navy;"></td></tr></span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1606" style="width: 35px; color: rgba(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="1715" style="width: 35px; color: rgba(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">@@ -1606,7 +1715,7 @@ order as they did in the input.</td>
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1606
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1715
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<pre style="margin: 0;"> <span id="LC1715" class="line" lang="markdown">Write unpaired reads that align at least once to file at <span class="sb" style="color: #d14;">`<path>`</span>. These reads</span>
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<pre style="margin: 0;"> <span id="LC1716" class="line" lang="markdown">correspond to the SAM records with the FLAGS <span class="sb" style="color: #d14;">`0x4`</span>, <span class="sb" style="color: #d14;">`0x40`</span>, and <span class="sb" style="color: #d14;">`0x80`</span> bits</span>
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<pre style="margin: 0;"> <span id="LC1717" class="line" lang="markdown">unset. If <span class="sb" style="color: #d14;">`--al-gz`</span> is specified, output will be gzip compressed. If <span class="sb" style="color: #d14;">`--al-bz2`</span></span>
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1609
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<pre style="margin: 0;">-<span id="LC1609" class="line" lang="markdown">is specified, output will be bzip2 compressed. Similarly if <span class="sb" style="color: #d14;">`--al-lz4`</span> is specified,<span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC1718" class="line" lang="markdown">is specified, output will be bzip2 compressed. Similarly if <span class="sb" style="color: #d14;">`--al-lz4`</span> is specified,</span>
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<pre style="margin: 0;"> <span id="LC1719" class="line" lang="markdown">output will be lz4 compressed. Reads written in this way will</span>
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<pre style="margin: 0;"> <span id="LC1720" class="line" lang="markdown">appear exactly as they did in the input file, without any modification (same</span>
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<pre style="margin: 0;"> <span id="LC1721" class="line" lang="markdown">sequence, same name, same quality string, same quality encoding). Reads will</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1768" style="width: 35px; color: rgba(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="1877" style="width: 35px; color: rgba(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">@@ -1768,13 +1877,14 @@ and `QUAL` strings. Specifying this option causes Bowtie 2 to print an asterisk</td>
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1768
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<pre style="margin: 0;"> <span id="LC1877" class="line" lang="markdown">in those fields instead.</span>
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<pre style="margin: 0;"> <span id="LC1878" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC1879" class="line" lang="markdown"><span class="nt" style="color: navy;"></td></tr></span></span>
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<pre style="margin: 0;">-<span id="LC1771" class="line" lang="markdown"><span class="nt" style="color: navy;"><tr><td</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"bowtie2-options-soft-clipped-unmapped-tlen<span class="idiff left right">-sec-seq</span>"</span><span class="nt" style="color: navy;">></span></span>
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<pre style="margin: 0;">+<span id="LC1880" class="line" lang="markdown"><span class="nt" style="color: navy;"><tr><td</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"bowtie2-options-soft-clipped-unmapped-tlen"</span><span class="nt" style="color: navy;">></span></span>
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<pre style="margin: 0;"> <span id="LC1881" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC1882" class="line" lang="markdown"><span class="sb" style="color: #d14;"> --soft-clipped-unmapped-tlen</span></span>
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<pre style="margin: 0;"> <span id="LC1884" class="line" lang="markdown"><span class="nt" style="color: navy;"></td><td></span></span>
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<pre style="margin: 0;">-<span id="LC1777" class="line" lang="markdown">Consider soft-clipped bases unmapped when calculating <span class="sb" style="color: #d14;">`TLEN`</span>.</span>
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<pre style="margin: 0;">+<span id="LC1886" class="line" lang="markdown">Consider soft-clipped bases unmapped when calculating <span class="sb" style="color: #d14;">`TLEN`</span>. Only available</span>
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<pre style="margin: 0;">+<span id="LC1887" class="line" lang="markdown">in <span class="p">[</span><span class="nv" style="color: teal;">`--local`</span><span class="p">]</span> mode.</span>
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1888
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<pre style="margin: 0;"> <span id="LC1888" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC1889" class="line" lang="markdown"><span class="nt" style="color: navy;"></td></tr></span></span>
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<pre style="margin: 0;"> <span id="LC1890" class="line" lang="markdown"><span class="nt" style="color: navy;"><tr><td</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"bowtie2-options-sam-no-qname-trunc"</span><span class="nt" style="color: navy;">></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">@@ -1923,10 +2033,10 @@ Print usage information and quit.</td>
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<pre style="margin: 0;"> <span id="LC2033" class="line" lang="markdown"><span class="gh" style="color: #999;">SAM output</span></span>
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<pre style="margin: 0;"> <span id="LC2034" class="line" lang="markdown"><span class="gh" style="color: #999;">----------</span></span>
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2035
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<pre style="margin: 0;"> <span id="LC2035" class="line" lang="markdown"></span>
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1926
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<pre style="margin: 0;">-<span id="LC1926" class="line" lang="markdown">Following is a brief description of the <span class="p">[</span><span class="nv" style="color: teal;">SAM</span><span class="p">]</span> format as output by <span class="sb" style="color: #d14;">`bowtie2`</span>.<span class="idiff left right"> </span></span>
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2036
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<pre style="margin: 0;">+<span id="LC2036" class="line" lang="markdown">Following is a brief description of the <span class="p">[</span><span class="nv" style="color: teal;">SAM</span><span class="p">]</span> format as output by <span class="sb" style="color: #d14;">`bowtie2`</span>.</span>
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1927
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2037
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<pre style="margin: 0;"> <span id="LC2037" class="line" lang="markdown">For more details, see the <span class="p">[</span><span class="nv" style="color: teal;">SAM format specification</span><span class="p">][</span><span class="ss" style="color: #990073;">SAM</span><span class="p">]</span>.</span>
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1928
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2038
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<pre style="margin: 0;"> <span id="LC2038" class="line" lang="markdown"></span>
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1929
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<pre style="margin: 0;">-<span id="LC1929" class="line" lang="markdown">By default, <span class="sb" style="color: #d14;">`bowtie2`</span> prints a SAM header with <span class="sb" style="color: #d14;">`@HD`</span>, <span class="sb" style="color: #d14;">`@SQ`</span> and <span class="sb" style="color: #d14;">`@PG`</span> lines.<span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC2039" class="line" lang="markdown">By default, <span class="sb" style="color: #d14;">`bowtie2`</span> prints a SAM header with <span class="sb" style="color: #d14;">`@HD`</span>, <span class="sb" style="color: #d14;">`@SQ`</span> and <span class="sb" style="color: #d14;">`@PG`</span> lines.</span>
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1930
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2040
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<pre style="margin: 0;"> <span id="LC2040" class="line" lang="markdown">When one or more <span class="p">[</span><span class="nv" style="color: teal;">`--rg`</span><span class="p">]</span> arguments are specified, <span class="sb" style="color: #d14;">`bowtie2`</span> will also print</span>
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1931
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2041
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<pre style="margin: 0;"> <span id="LC2041" class="line" lang="markdown">an <span class="sb" style="color: #d14;">`@RG`</span> line that includes all user-specified <span class="p">[</span><span class="nv" style="color: teal;">`--rg`</span><span class="p">]</span> tokens separated by</span>
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1932
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2042
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<pre style="margin: 0;"> <span id="LC2042" class="line" lang="markdown">tabs.</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">@@ -2088,7 +2198,7 @@ alignment.</td>
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2198
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<pre style="margin: 0;"> <span id="LC2198" class="line" lang="markdown"></span>
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2199
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<pre style="margin: 0;"> <span id="LC2199" class="line" lang="markdown"><span class="nt" style="color: navy;"></td><td></span></span>
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2090
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2200
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<pre style="margin: 0;"> <span id="LC2200" class="line" lang="markdown"></span>
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2091
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<pre style="margin: 0;">-<span id="LC2091" class="line" lang="markdown">The number of ambiguous bases in the reference covering this alignment.<span class="idiff left right"> </span></span>
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2201
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<pre style="margin: 0;">+<span id="LC2201" class="line" lang="markdown">The number of ambiguous bases in the reference covering this alignment.</span>
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2092
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2202
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<pre style="margin: 0;"> <span id="LC2202" class="line" lang="markdown">Only present if SAM record is for an aligned read.</span>
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2093
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2203
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<pre style="margin: 0;"> <span id="LC2203" class="line" lang="markdown"></span>
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2094
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2204
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<pre style="margin: 0;"> <span id="LC2204" class="line" lang="markdown"><span class="nt" style="color: navy;"></td></tr><tr><td</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"bowtie2-build-opt-fields-xm"</span><span class="nt" style="color: navy;">></span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2266" style="width: 35px; color: rgba(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">@@ -2156,7 +2266,7 @@ pair failed to aligned either concordantly or discordantly.</td>
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2156
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2266
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<pre style="margin: 0;"> <span id="LC2266" class="line" lang="markdown"></span>
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2157
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2267
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<pre style="margin: 0;"> <span id="LC2267" class="line" lang="markdown"><span class="nt" style="color: navy;"></td><td></span></span>
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2268
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<pre style="margin: 0;"> <span id="LC2268" class="line" lang="markdown"></span>
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2159
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<pre style="margin: 0;">-<span id="LC2159" class="line" lang="markdown">A string representation of the mismatched reference bases in the alignment.<span class="idiff left right"> </span></span>
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2269
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<pre style="margin: 0;">+<span id="LC2269" class="line" lang="markdown">A string representation of the mismatched reference bases in the alignment.</span>
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2160
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<pre style="margin: 0;"> <span id="LC2270" class="line" lang="markdown">See <span class="p">[</span><span class="nv" style="color: teal;">SAM Tags format specification</span><span class="p">][</span><span class="ss" style="color: #990073;">SAMTags</span><span class="p">]</span> for details. Only present if SAM record is</span>
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2161
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2271
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<pre style="margin: 0;"> <span id="LC2271" class="line" lang="markdown">for an aligned read.</span>
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2162
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2272
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<pre style="margin: 0;"> <span id="LC2272" class="line" lang="markdown"></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2279" style="width: 35px; color: rgba(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">@@ -2169,7 +2279,7 @@ The `bowtie2-build` indexer</td>
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2279
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<pre style="margin: 0;"> <span id="LC2279" class="line" lang="markdown"></span>
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2170
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2280
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<pre style="margin: 0;"> <span id="LC2280" class="line" lang="markdown"><span class="sb" style="color: #d14;">`bowtie2-build`</span> builds a Bowtie index from a set of DNA sequences.</span>
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2171
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2281
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<pre style="margin: 0;"> <span id="LC2281" class="line" lang="markdown"><span class="sb" style="color: #d14;">`bowtie2-build`</span> outputs a set of 6 files with suffixes <span class="sb" style="color: #d14;">`.1.bt2`</span>, <span class="sb" style="color: #d14;">`.2.bt2`</span>,</span>
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2172
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<pre style="margin: 0;">-<span id="LC2172" class="line" lang="markdown"><span class="sb" style="color: #d14;">`.3.bt2`</span>, <span class="sb" style="color: #d14;">`.4.bt2`</span>, <span class="sb" style="color: #d14;">`.rev.1.bt2`</span>, and <span class="sb" style="color: #d14;">`.rev.2.bt2`</span>. In the case of a large<span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC2282" class="line" lang="markdown"><span class="sb" style="color: #d14;">`.3.bt2`</span>, <span class="sb" style="color: #d14;">`.4.bt2`</span>, <span class="sb" style="color: #d14;">`.rev.1.bt2`</span>, and <span class="sb" style="color: #d14;">`.rev.2.bt2`</span>. In the case of a large</span>
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2173
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<pre style="margin: 0;"> <span id="LC2283" class="line" lang="markdown">index these suffixes will have a <span class="sb" style="color: #d14;">`bt2l`</span> termination. These files together</span>
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2174
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2284
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<pre style="margin: 0;"> <span id="LC2284" class="line" lang="markdown">constitute the index: they are all that is needed to align reads to that</span>
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2175
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2285
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<pre style="margin: 0;"> <span id="LC2285" class="line" lang="markdown">reference. The original sequence <span class="p">[</span><span class="nv" style="color: teal;">`FASTA`</span><span class="p">]</span> files are no longer used by Bowtie 2</span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2407" style="width: 35px; color: rgba(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">@@ -2297,7 +2407,7 @@ automatically by default; use [`-a`/`--noauto`] to configure manually.</td>
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2297
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2407
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<pre style="margin: 0;"> <span id="LC2407" class="line" lang="markdown"></span>
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2298
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2408
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<pre style="margin: 0;"> <span id="LC2408" class="line" lang="markdown">The maximum number of suffixes allowed in a block. Allowing more suffixes per</span>
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2299
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2409
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<pre style="margin: 0;"> <span id="LC2409" class="line" lang="markdown">block makes indexing faster, but increases peak memory usage. Setting this</span>
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2300
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<pre style="margin: 0;">-<span id="LC2300" class="line" lang="markdown">option overrides any previous setting for <span class="p">[</span><span class="nv" style="color: teal;">`--bmax`</span><span class="p">]</span>, or <span class="p">[</span><span class="nv" style="color: teal;">`--bmaxdivn`</span><span class="p">]</span>.<span class="idiff left right"> </span></span>
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2410
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<pre style="margin: 0;">+<span id="LC2410" class="line" lang="markdown">option overrides any previous setting for <span class="p">[</span><span class="nv" style="color: teal;">`--bmax`</span><span class="p">]</span>, or <span class="p">[</span><span class="nv" style="color: teal;">`--bmaxdivn`</span><span class="p">]</span>.</span>
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2301
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2411
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<pre style="margin: 0;"> <span id="LC2411" class="line" lang="markdown">Default (in terms of the <span class="p">[</span><span class="nv" style="color: teal;">`--bmaxdivn`</span><span class="p">]</span> parameter) is <span class="p">[</span><span class="nv" style="color: teal;">`--bmaxdivn`</span><span class="p">]</span> 4 <span class="err" style="color: #a61717; background-color: #e3d2d2;">*</span> number of threads. This is</span>
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2302
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2412
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<pre style="margin: 0;"> <span id="LC2412" class="line" lang="markdown">configured automatically by default; use <span class="p">[</span><span class="nv" style="color: teal;">`-a`/`--noauto`</span><span class="p">]</span> to configure manually.</span>
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2303
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2413
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<pre style="margin: 0;"> <span id="LC2413" class="line" lang="markdown"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2362" style="width: 35px; color: rgba(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="2472" style="width: 35px; color: rgba(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">@@ -2362,7 +2472,7 @@ paired-end alignment.</td>
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2362
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2472
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<pre style="margin: 0;"> <span id="LC2472" class="line" lang="markdown"></span>
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2363
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<pre style="margin: 0;"> <span id="LC2473" class="line" lang="markdown">To map alignments back to positions on the reference sequences, it's necessary</span>
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<pre style="margin: 0;"> <span id="LC2474" class="line" lang="markdown">to annotate ("mark") some or all of the <span class="p">[</span><span class="nv" style="color: teal;">Burrows-Wheeler</span><span class="p">]</span> rows with their</span>
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2365
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<pre style="margin: 0;">-<span id="LC2365" class="line" lang="markdown">corresponding location on the genome.<span class="idiff left right"> </span></span>
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2475
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<pre style="margin: 0;">+<span id="LC2475" class="line" lang="markdown">corresponding location on the genome.</span>
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2366
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2476
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<pre style="margin: 0;"> <span id="LC2476" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: teal;">`-o`/`--offrate`</span><span class="p">](</span><span class="sx" style="color: #d14;">#bowtie2-build-options-o</span><span class="p">)</span> governs how many rows get marked:</span>
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2367
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2477
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<pre style="margin: 0;"> <span id="LC2477" class="line" lang="markdown">the indexer will mark every 2^<span class="sb" style="color: #d14;">`<int>`</span> rows. Marking more rows makes</span>
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2368
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2478
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<pre style="margin: 0;"> <span id="LC2478" class="line" lang="markdown">reference-position lookups faster, but requires more memory to hold the</span>
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<td class="diff-line-num unfold js-unfold old_line" 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">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2524" style="width: 35px; color: rgba(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">@@ -2414,7 +2524,7 @@ print only error messages.</td>
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2414
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2524
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<pre style="margin: 0;"> <span id="LC2524" class="line" lang="markdown"></span>
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2415
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2525
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<pre style="margin: 0;"> <span id="LC2525" class="line" lang="markdown">By default <span class="sb" style="color: #d14;">`bowtie2-build`</span> is using only one thread. Increasing the number</span>
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2416
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2526
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<pre style="margin: 0;"> <span id="LC2526" class="line" lang="markdown">of threads will speed up the index building considerably in most cases.</span>
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2417
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<td class="diff-line-num new_line old" data-linenumber="2527" 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="LC2417" class="line" lang="markdown"><span class="idiff left right"> </span></span>
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2527
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<pre style="margin: 0;">+<span id="LC2527" class="line" lang="markdown"></span>
</pre>
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2418
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<td class="diff-line-num new_line" data-linenumber="2528" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2528
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<pre style="margin: 0;"> <span id="LC2528" class="line" lang="markdown"><span class="nt" style="color: navy;"></td></tr><tr><td></span></span>
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2419
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2529
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<pre style="margin: 0;"> <span id="LC2529" class="line" lang="markdown"></span>
</pre>
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2420
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<td class="diff-line-num new_line" data-linenumber="2530" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2530
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<pre style="margin: 0;"> <span id="LC2530" class="line" lang="markdown"><span class="sb" style="color: #d14;"> -h/--help</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2492" style="width: 35px; color: rgba(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="2602" style="width: 35px; color: rgba(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">@@ -2492,7 +2602,7 @@ Print reference sequence names, one per line, and quit.</td>
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<td class="diff-line-num old_line" data-linenumber="2492" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2492
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2602
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<pre style="margin: 0;"> <span id="LC2602" class="line" lang="markdown"><span class="nt" style="color: navy;"></td><td></span></span>
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<td class="diff-line-num old_line" data-linenumber="2493" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2493
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<td class="diff-line-num new_line" data-linenumber="2603" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2603
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<pre style="margin: 0;"> <span id="LC2603" class="line" lang="markdown"></span>
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<td class="diff-line-num old_line" data-linenumber="2494" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2494
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<td class="diff-line-num new_line" data-linenumber="2604" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2604
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<pre style="margin: 0;"> <span id="LC2604" class="line" lang="markdown">Print a summary that includes information about index settings, as well as the</span>
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2495
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<td class="diff-line-num new_line old" data-linenumber="2605" 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="LC2495" class="line" lang="markdown">names and lengths of the input sequences. The summary has this format:<span class="idiff left right"> </span></span>
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<td class="diff-line-num new old_line" data-linenumber="2496" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="2605" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2605
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<pre style="margin: 0;">+<span id="LC2605" class="line" lang="markdown">names and lengths of the input sequences. The summary has this format:</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2496" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2496
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<td class="diff-line-num new_line" data-linenumber="2606" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2606
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<pre style="margin: 0;"> <span id="LC2606" class="line" lang="markdown"></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2497
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<td class="diff-line-num new_line" data-linenumber="2607" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2607
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<pre style="margin: 0;"> <span id="LC2607" class="line" lang="markdown"><span class="sb" style="color: #d14;"> Colorspace <0 or 1></span></span>
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<td class="diff-line-num old_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">
2498
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<td class="diff-line-num new_line" data-linenumber="2608" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2608
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<pre style="margin: 0;"> <span id="LC2608" class="line" lang="markdown"><span class="sb" style="color: #d14;"> SA-Sample 1 in <sample></span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2719" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2829" style="width: 35px; color: rgba(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">@@ -2719,7 +2829,6 @@ for more details and variations on this process.</td>
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<td class="diff-line-num old_line" data-linenumber="2719" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2719
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<td class="diff-line-num new_line" data-linenumber="2829" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2829
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<pre style="margin: 0;"> <span id="LC2829" class="line" lang="markdown"><span class="p">[</span><span class="ss" style="color: #990073;">Threading Building Blocks library</span><span class="p">]:</span> <span class="sx" style="color: #d14;">https://www.threadingbuildingblocks.org</span></span>
</pre>
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<tr class="line_holder" id="" style="line-height: 1.6;">
<td class="diff-line-num old_line" data-linenumber="2720" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2720
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<td class="diff-line-num new_line" data-linenumber="2830" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2830
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<pre style="margin: 0;"> <span id="LC2830" class="line" lang="markdown"><span class="p">[</span><span class="ss" style="color: #990073;">TopHat</span><span class="p">]:</span> <span class="sx" style="color: #d14;">http://tophat.cbcb.umd.edu/</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2721" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2721
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<td class="diff-line-num new_line" data-linenumber="2831" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2831
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<pre style="margin: 0;"> <span id="LC2831" class="line" lang="markdown"><span class="p">[</span><span class="ss" style="color: #990073;">UCSC</span><span class="p">]:</span> <span class="sx" style="color: #d14;">http://genome.ucsc.edu/cgi-bin/hgGateway</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="2722" 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">
2722
</td>
<td class="diff-line-num new_line old" data-linenumber="2832" 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="LC2722" class="line" lang="markdown"><span class="p">[</span><span class="ss" style="color: #990073;">Vmatch</span><span class="p">]:</span> <span class="sx" style="color: #d14;">http://www.vmatch.de/</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2723" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2723
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<td class="diff-line-num new_line" data-linenumber="2832" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2832
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<pre style="margin: 0;"> <span id="LC2832" class="line" lang="markdown"><span class="p">[</span><span class="ss" style="color: #990073;">Xcode</span><span class="p">]:</span> <span class="sx" style="color: #d14;">http://developer.apple.com/xcode/</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2724" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2724
</td>
<td class="diff-line-num new_line" data-linenumber="2833" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2833
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<pre style="margin: 0;"> <span id="LC2833" class="line" lang="markdown"><span class="p">[</span><span class="ss" style="color: #990073;">`+I`/`--minins`</span><span class="p">]:</span> <span class="sx" style="color: #d14;">#bowtie2-options-I</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2725" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2725
</td>
<td class="diff-line-num new_line" data-linenumber="2834" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2834
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<pre style="margin: 0;"> <span id="LC2834" class="line" lang="markdown"><span class="p">[</span><span class="ss" style="color: #990073;">`+I`</span><span class="p">]:</span> <span class="sx" style="color: #d14;">#bowtie2-options-I</span></span>
</pre>
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<tr class="line_holder match" id="" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2815" style="width: 35px; color: rgba(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="2924" style="width: 35px; color: rgba(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">@@ -2815,6 +2924,7 @@ for more details and variations on this process.</td>
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<td class="diff-line-num old_line" data-linenumber="2815" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2815
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<td class="diff-line-num new_line" data-linenumber="2924" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2924
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<pre style="margin: 0;"> <span id="LC2924" class="line" lang="markdown"><span class="p">[</span><span class="ss" style="color: #990073;">`-3`</span><span class="p">]:</span> <span class="sx" style="color: #d14;">#bowtie2-options-3</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2816" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2816
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2925
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<pre style="margin: 0;"> <span id="LC2925" class="line" lang="markdown"><span class="p">[</span><span class="ss" style="color: #990073;">`-5`/`--trim5`</span><span class="p">]:</span> <span class="sx" style="color: #d14;">#bowtie2-options-5</span></span>
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2817
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2926
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<pre style="margin: 0;"> <span id="LC2926" class="line" lang="markdown"><span class="p">[</span><span class="ss" style="color: #990073;">`-5`</span><span class="p">]:</span> <span class="sx" style="color: #d14;">#bowtie2-options-5</span></span>
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2927
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<pre style="margin: 0;">+<span id="LC2927" class="line" lang="markdown"><span class="p">[</span><span class="ss" style="color: #990073;">`--trim-to`</span><span class="p">]:</span> <span class="sx" style="color: #d14;">#bowtie2-options-trim-to</span></span>
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2818
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2928
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<pre style="margin: 0;"> <span id="LC2928" class="line" lang="markdown"><span class="p">[</span><span class="ss" style="color: #990073;">`-D`</span><span class="p">]:</span> <span class="sx" style="color: #d14;">#bowtie2-options-D</span></span>
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2819
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2929
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<pre style="margin: 0;"> <span id="LC2929" class="line" lang="markdown"><span class="p">[</span><span class="ss" style="color: #990073;">`-L`</span><span class="p">]:</span> <span class="sx" style="color: #d14;">#bowtie2-options-L</span></span>
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2820
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2930
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<pre style="margin: 0;"> <span id="LC2930" class="line" lang="markdown"><span class="p">[</span><span class="ss" style="color: #990073;">`-N`</span><span class="p">]:</span> <span class="sx" style="color: #d14;">#bowtie2-options-N</span></span>
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<li id="836efb6e25a091dcb4ff8e1dbb2f0be6a5cbf14c">
<a href="https://salsa.debian.org/med-team/bowtie2/commit/157dbc209f47672a9a7167d16e3a324803906000#836efb6e25a091dcb4ff8e1dbb2f0be6a5cbf14c"><strong>Makefile</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">@@ -36,9 +36,9 @@ HEADERS := $(wildcard *.h)</td>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="make"><span class="nv" style="color: teal;">BOWTIE_MM</span> <span class="o" style="font-weight: 600;">:=</span> 1</span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="make"><span class="nv" style="color: teal;">BOWTIE_SHARED_MEM</span> <span class="o" style="font-weight: 600;">:=</span></span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="make"></span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">ifdef</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff left right">RELEASE</span>_BUILD</span></span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="make"> <span class="nv" style="color: teal;">LDFLAGS</span> <span class="o" style="font-weight: 600;">+=</span> <span class="nt" style="color: navy;">-L</span><span class="nv" style="color: teal;">$(CURDIR)</span>/.lib</span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="make"> <span class="nv" style="color: teal;">CPPFLAGS</span> <span class="o" style="font-weight: 600;">+=</span> <span class="nt" style="color: navy;">-I</span><span class="nv" style="color: teal;">$(CURDIR)</span>/.include</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">ifdef</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff left right">STATIC</span>_BUILD</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="make"> <span class="nv" style="color: teal;">LDFLAGS</span> <span class="o" style="font-weight: 600;">+=</span> <span class="nt" style="color: navy;">-L</span><span class="nv" style="color: teal;">$(CURDIR)</span>/.<span class="idiff left right">tmp/</span>lib</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="make"> <span class="nv" style="color: teal;">CPPFLAGS</span> <span class="o" style="font-weight: 600;">+=</span> <span class="nt" style="color: navy;">-I</span><span class="nv" style="color: teal;">$(CURDIR)</span>/.<span class="idiff left right">tmp/</span>include</span>
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42
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">endif</span></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="make"></span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># Detect Cygwin or MinGW</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="58" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="58" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -58,7 +58,7 @@ ifneq (,$(findstring Darwin,$(shell uname)))</td>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="make"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">ifeq</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">(1,$(shell</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">uname</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-r</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">|</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">awk</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-F.</span> <span class="s1" style="color: #d14;">'{ if ($$1 > 12 && $$1 < 16) print 1; }'</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">))</span></span>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="make"> <span class="nv" style="color: teal;">CXXFLAGS</span> <span class="o" style="font-weight: 600;">+=</span> <span class="nt" style="color: navy;">-stdlib</span><span class="o" style="font-weight: 600;">=</span>libstdc++</span>
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60
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="make"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">endif</span></span>
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61
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="make"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">ifdef</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff left right">RELEASE</span>_BUILD</span></span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="make"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">ifdef</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff left right">STATIC</span>_BUILD</span></span>
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62
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62
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="make"> <span class="nv" style="color: teal;">CXXFLAGS</span> <span class="o" style="font-weight: 600;">+=</span> <span class="nt" style="color: navy;">-mmacosx-version-min</span><span class="o" style="font-weight: 600;">=</span>10.9</span>
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63
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63
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="make"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">endif</span></span>
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64
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64
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">endif</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">@@ -102,7 +102,7 @@ endif</td>
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102
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102
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<pre style="margin: 0;"> <span id="LC102" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;">#default is to use Intel TBB</span></span>
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103
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103
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">ifneq</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">(1,$(NO_TBB))</span></span>
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<td class="diff-line-num old_line" data-linenumber="104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
104
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104
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<pre style="margin: 0;"> <span id="LC104" class="line" lang="make"> <span class="nv" style="color: teal;">LDLIBS</span> <span class="o" style="font-weight: 600;">+=</span> <span class="nv" style="color: teal;">$(PTHREAD_LIB)</span> <span class="nt" style="color: navy;">-ltbb</span></span>
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105
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<pre style="margin: 0;">-<span id="LC105" class="line" lang="make"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">ifdef</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff left right">RELEASE</span>_BUILD</span></span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="make"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">ifdef</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff left right">STATIC</span>_BUILD</span></span>
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106
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<pre style="margin: 0;"> <span id="LC106" class="line" lang="make"> <span class="nv" style="color: teal;">LDLIBS</span> <span class="o" style="font-weight: 600;">+=</span> <span class="nt" style="color: navy;">-ltbbmalloc</span></span>
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107
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107
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<pre style="margin: 0;"> <span id="LC107" class="line" lang="make"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">else</span></span>
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108
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108
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<pre style="margin: 0;"> <span id="LC108" class="line" lang="make"> <span class="nv" style="color: teal;">LDLIBS</span> <span class="o" style="font-weight: 600;">+=</span> <span class="nt" style="color: navy;">-ltbbmalloc_proxy</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">@@ -443,8 +443,8 @@ bowtie2-inspect.bat:</td>
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443
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443
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<pre style="margin: 0;"> <span id="LC443" class="line" lang="make"> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"@echo off"</span> <span class="o" style="font-weight: 600;">></span> bowtie2-inspect.bat</span>
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444
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444
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<pre style="margin: 0;"> <span id="LC444" class="line" lang="make"> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"python %~dp0/bowtie2-inspect %*"</span> <span class="o" style="font-weight: 600;">>></span> bowtie2-inspect.bat</span>
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445
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445
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<pre style="margin: 0;"> <span id="LC445" class="line" lang="make"></span>
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446
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<pre style="margin: 0;">-<span id="LC446" class="line" lang="make"><span class="nl">.PHONY</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">bowtie2-src</span></span>
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447
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<pre style="margin: 0;">-<span id="LC447" class="line" lang="make"><span class="nl">bowtie2-src</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">$(SRC_PKG_LIST)</span></span>
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446
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<pre style="margin: 0;">+<span id="LC446" class="line" lang="make"><span class="nl">.PHONY</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">bowtie2-src<span class="idiff left right">-pkg</span></span></span>
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447
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<pre style="margin: 0;">+<span id="LC447" class="line" lang="make"><span class="nl">bowtie2-src<span class="idiff left right">-pkg</span></span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">$(SRC_PKG_LIST)</span></span>
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448
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448
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<pre style="margin: 0;"> <span id="LC448" class="line" lang="make"> <span class="nb" style="color: #0086b3;">chmod </span>a+x scripts/<span class="k" style="font-weight: 600;">*</span>.sh scripts/<span class="k" style="font-weight: 600;">*</span>.pl</span>
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<pre style="margin: 0;"> <span id="LC449" class="line" lang="make"> <span class="nb" style="color: #0086b3;">mkdir</span> .src.tmp</span>
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<pre style="margin: 0;"> <span id="LC450" class="line" lang="make"> <span class="nb" style="color: #0086b3;">mkdir</span> .src.tmp/bowtie2-<span class="nv" style="color: teal;">$(VERSION)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="455" style="width: 35px; color: rgba(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="455" style="width: 35px; color: rgba(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">@@ -455,9 +455,9 @@ bowtie2-src: $(SRC_PKG_LIST)</td>
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455
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<pre style="margin: 0;"> <span id="LC455" class="line" lang="make"> <span class="nb" style="color: #0086b3;">cp</span> .src.tmp/bowtie2-<span class="nv" style="color: teal;">$(VERSION)</span><span class="nt" style="color: navy;">-source</span>.zip .</span>
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<pre style="margin: 0;"> <span id="LC456" class="line" lang="make"> <span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: navy;">-rf</span> .src.tmp</span>
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<pre style="margin: 0;"> <span id="LC457" class="line" lang="make"></span>
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<pre style="margin: 0;">-<span id="LC458" class="line" lang="make"><span class="nl">.PHONY</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">bowtie2-pkg</span></span>
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459
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<pre style="margin: 0;">-<span id="LC459" class="line" lang="make"><span class="nl">bowtie2-pkg</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">PKG_DIR := bowtie2-$(VERSION)-$(if $(MACOS)</span><span class="p">,</span><span class="nf" style="color: #900; font-weight: 600;">macos</span><span class="p">,</span><span class="nf" style="color: #900; font-weight: 600;">$(if $(MINGW)</span><span class="p">,</span><span class="nf" style="color: #900; font-weight: 600;">mingw</span><span class="p">,</span><span class="nf" style="color: #900; font-weight: 600;">linux))-x86_64</span></span>
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460
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<pre style="margin: 0;">-<span id="LC460" class="line" lang="make"><span class="nl">bowtie2-pkg</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">static-libs $(BIN_PKG_LIST) $(BOWTIE2_BIN_LIST) $(BOWTIE2_BIN_LIST_DBG)</span></span>
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458
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<pre style="margin: 0;">+<span id="LC458" class="line" lang="make"><span class="nl">.PHONY</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">bowtie2-<span class="idiff left right">bin-</span>pkg</span></span>
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<pre style="margin: 0;">+<span id="LC459" class="line" lang="make"><span class="nl">bowtie2-<span class="idiff left right">bin-</span>pkg</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">PKG_DIR := bowtie2-$(VERSION)-$(if $(MACOS)</span><span class="p">,</span><span class="nf" style="color: #900; font-weight: 600;">macos</span><span class="p">,</span><span class="nf" style="color: #900; font-weight: 600;">$(if $(MINGW)</span><span class="p">,</span><span class="nf" style="color: #900; font-weight: 600;">mingw</span><span class="p">,</span><span class="nf" style="color: #900; font-weight: 600;">linux))-x86_64</span></span>
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<pre style="margin: 0;">+<span id="LC460" class="line" lang="make"><span class="nl">bowtie2-<span class="idiff left right">bin-</span>pkg</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">static-libs $(BIN_PKG_LIST) $(BOWTIE2_BIN_LIST) $(BOWTIE2_BIN_LIST_DBG)</span></span>
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461
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<pre style="margin: 0;"> <span id="LC461" class="line" lang="make"> <span class="nb" style="color: #0086b3;">chmod </span>a+x scripts/<span class="k" style="font-weight: 600;">*</span>.sh scripts/<span class="k" style="font-weight: 600;">*</span>.pl</span>
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<pre style="margin: 0;"> <span id="LC462" class="line" lang="make"> <span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: navy;">-rf</span> .bin.tmp</span>
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<pre style="margin: 0;"> <span id="LC463" class="line" lang="make"> <span class="nb" style="color: #0086b3;">mkdir</span> <span class="nt" style="color: navy;">-p</span> .bin.tmp/<span class="nv" style="color: teal;">$(PKG_DIR)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="487" style="width: 35px; color: rgba(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">@@ -487,8 +487,9 @@ doc: doc/manual.html MANUAL</td>
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<pre style="margin: 0;"> <span id="LC487" class="line" lang="make"></span>
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<pre style="margin: 0;"> <span id="LC488" class="line" lang="make"><span class="nl">doc/manual.html</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">MANUAL.markdown</span></span>
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489
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<pre style="margin: 0;"> <span id="LC489" class="line" lang="make"> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"<h1>Table of Contents</h1>"</span> <span class="o" style="font-weight: 600;">></span> .tmp.head</span>
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<pre style="margin: 0;">-<span id="LC490" class="line" lang="make"> pandoc <span class="nt" style="color: navy;">-T</span> <span class="s2" style="color: #d14;">"Bowtie 2 Manual"</span> <span class="nt" style="color: navy;">-B</span> .tmp.head <span class="se" style="color: #d14;">\</span></span>
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491
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<pre style="margin: 0;">-<span id="LC491" class="line" lang="make"> <span class="nt" style="color: navy;">--css</span> style.css <span class="nt" style="color: navy;">-o</span> <span class="nv" style="color: teal;">$@</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC490" class="line" lang="make"> pandoc <span class="nt" style="color: navy;">-B</span> .tmp.head <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC491" class="line" lang="make"> <span class="nt" style="color: navy;">--metadata</span> title:<span class="s2" style="color: #d14;">"Bowtie 2 Manual"</span><span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC492" class="line" lang="make"> <span class="nt" style="color: navy;">--css</span> doc/style.css <span class="nt" style="color: navy;">-o</span> <span class="nv" style="color: teal;">$@</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;"> <span id="LC493" class="line" lang="make"> <span class="nt" style="color: navy;">--from</span> markdown <span class="nt" style="color: navy;">--to</span> HTML <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;"> <span id="LC494" class="line" lang="make"> <span class="nt" style="color: navy;">--table-of-contents</span> <span class="nv" style="color: teal;">$^</span></span>
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<pre style="margin: 0;"> <span id="LC495" class="line" lang="make"> <span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: navy;">-f</span> .tmp.head</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -505,41 +506,42 @@ install: all</td>
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<pre style="margin: 0;"> <span id="LC506" class="line" lang="make"></span>
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<pre style="margin: 0;"> <span id="LC507" class="line" lang="make"><span class="nl">.PHONY</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">simple-test</span></span>
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507
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508
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<pre style="margin: 0;"> <span id="LC508" class="line" lang="make"><span class="nl">simple-test</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">perl-deps both both-debug both-sanitized</span></span>
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508
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<pre style="margin: 0;">-<span id="LC508" class="line" lang="make"> <span class="nb" style="color: #0086b3;">eval</span> <span class="sb" style="color: #d14;">`</span>perl <span class="nt" style="color: navy;">-I</span> <span class="nv" style="color: teal;">$(CURDIR)</span>/.<span class="idiff left">perllib.tmp/lib/perl5 </span><span class="nt" style="color: navy;"><span class="idiff">-Mlocal</span></span><span class="idiff">::lib</span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="nv" style="color: teal;"><span class="idiff">$(CURDIR)</span></span><span class="idiff right">/.perllib</span>.tmp<span class="sb" style="color: #d14;">`</span> <span class="p">;</span> <span class="se" style="color: #d14;">\</span></span>
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509
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<pre style="margin: 0;">+<span id="LC509" class="line" lang="make"> <span class="nb" style="color: #0086b3;">eval</span> <span class="sb" style="color: #d14;">`</span>perl <span class="nt" style="color: navy;">-I</span> <span class="nv" style="color: teal;">$(CURDIR)</span>/.<span class="idiff left">tmp/lib/perl5 </span><span class="nt" style="color: navy;"><span class="idiff">-Mlocal</span></span><span class="idiff">::lib</span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="nv" style="color: teal;"><span class="idiff">$(CURDIR)</span></span><span class="idiff right">/</span>.tmp<span class="sb" style="color: #d14;">`</span> <span class="p">;</span> <span class="se" style="color: #d14;">\</span></span>
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509
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<pre style="margin: 0;"> <span id="LC510" class="line" lang="make"> sh ./scripts/test/simple_tests.sh</span>
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511
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<pre style="margin: 0;"> <span id="LC511" class="line" lang="make"></span>
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<pre style="margin: 0;"> <span id="LC512" class="line" lang="make"><span class="nl">.PHONY</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">random-test</span></span>
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513
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<pre style="margin: 0;"> <span id="LC513" class="line" lang="make"><span class="nl">random-test</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">all perl-deps</span></span>
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<pre style="margin: 0;">-<span id="LC513" class="line" lang="make"> <span class="nb" style="color: #0086b3;">eval</span> <span class="sb" style="color: #d14;">`</span>perl <span class="nt" style="color: navy;">-I</span> <span class="nv" style="color: teal;">$(CURDIR)</span>/.<span class="idiff left">perllib.tmp/lib/perl5 </span><span class="nt" style="color: navy;"><span class="idiff">-Mlocal</span></span><span class="idiff">::lib</span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="nv" style="color: teal;"><span class="idiff">$(CURDIR)</span></span><span class="idiff right">/.perllib</span>.tmp<span class="sb" style="color: #d14;">`</span> <span class="p">;</span> <span class="se" style="color: #d14;">\</span></span>
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514
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<pre style="margin: 0;">+<span id="LC514" class="line" lang="make"> <span class="nb" style="color: #0086b3;">eval</span> <span class="sb" style="color: #d14;">`</span>perl <span class="nt" style="color: navy;">-I</span> <span class="nv" style="color: teal;">$(CURDIR)</span>/.<span class="idiff left">tmp/lib/perl5 </span><span class="nt" style="color: navy;"><span class="idiff">-Mlocal</span></span><span class="idiff">::lib</span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="nv" style="color: teal;"><span class="idiff">$(CURDIR)</span></span><span class="idiff right">/</span>.tmp<span class="sb" style="color: #d14;">`</span> <span class="p">;</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;"> <span id="LC515" class="line" lang="make"> sh ./scripts/sim/run.sh <span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="o" style="font-weight: 600;">(</span><span class="k" style="font-weight: 600;">if</span> <span class="nv" style="color: teal;">$(NUM_CORES)</span>, <span class="nv" style="color: teal;">$(NUM_CORES)</span>, 2<span class="o" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;"> <span id="LC516" class="line" lang="make"></span>
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<pre style="margin: 0;"> <span id="LC517" class="line" lang="make"><span class="nl">.PHONY</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">perl-deps</span></span>
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<pre style="margin: 0;"> <span id="LC518" class="line" lang="make"><span class="nl">perl-deps</span><span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;">-<span id="LC518" class="line" lang="make"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="o" style="font-weight: 600;">!</span> <span class="nt" style="color: navy;">-e</span> .<span class="idiff left right">perllib.</span>tmp <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span> <span class="se" style="color: #d14;">\</span></span>
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519
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<pre style="margin: 0;">+<span id="LC519" class="line" lang="make"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="o" style="font-weight: 600;">!</span> <span class="nt" style="color: navy;">-e</span> .tmp <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span> <span class="se" style="color: #d14;">\</span></span>
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519
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520
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<pre style="margin: 0;"> <span id="LC520" class="line" lang="make"> <span class="nv" style="color: teal;">DL</span><span class="o" style="font-weight: 600;">=</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">$$</span><span class="o" style="font-weight: 600;">([</span> <span class="sb" style="color: #d14;">`</span>which wget<span class="sb" style="color: #d14;">`</span> <span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"wget --no-check-certificate -O-"</span> <span class="o" style="font-weight: 600;">||</span> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"curl -L"</span><span class="o" style="font-weight: 600;">)</span> <span class="p">;</span> <span class="se" style="color: #d14;">\</span></span>
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520
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<pre style="margin: 0;">-<span id="LC520" class="line" lang="make"> <span class="nb" style="color: #0086b3;">mkdir</span> .<span class="idiff left right">perllib.</span>tmp <span class="p">;</span> <span class="se" style="color: #d14;">\</span></span>
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521
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<pre style="margin: 0;">-<span id="LC521" class="line" lang="make"> <span class="nv" style="color: teal;">$$</span>DL http://cpanmin.us | perl - <span class="nt" style="color: navy;">-l</span> <span class="nv" style="color: teal;">$(CURDIR)</span>/.<span class="idiff left right">perllib.</span>tmp App::cpanminus <span class="nb" style="color: #0086b3;">local</span>::lib <span class="p">;</span> <span class="se" style="color: #d14;">\</span></span>
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522
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<pre style="margin: 0;">-<span id="LC522" class="line" lang="make"> <span class="nb" style="color: #0086b3;">eval</span> <span class="sb" style="color: #d14;">`</span>perl <span class="nt" style="color: navy;">-I</span> <span class="nv" style="color: teal;">$(CURDIR)</span>/.<span class="idiff left">perllib.tmp/lib/perl5 </span><span class="nt" style="color: navy;"><span class="idiff">-Mlocal</span></span><span class="idiff">::lib</span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="nv" style="color: teal;"><span class="idiff">$(CURDIR)</span></span><span class="idiff right">/.perllib</span>.tmp<span class="sb" style="color: #d14;">`</span> <span class="p">;</span> <span class="se" style="color: #d14;">\</span></span>
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523
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<pre style="margin: 0;">-<span id="LC523" class="line" lang="make"> <span class="nv" style="color: teal;">$(CURDIR)</span>/.<span class="idiff left right">perllib.</span>tmp/bin/cpanm <span class="nt" style="color: navy;">--force</span> Math::Random Clone Test::Deep Sys::Info <span class="p">;</span> <span class="se" style="color: #d14;">\</span></span>
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521
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<pre style="margin: 0;">+<span id="LC521" class="line" lang="make"> <span class="nb" style="color: #0086b3;">mkdir</span> .tmp <span class="p">;</span> <span class="se" style="color: #d14;">\</span></span>
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522
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<pre style="margin: 0;">+<span id="LC522" class="line" lang="make"> <span class="nv" style="color: teal;">$$</span>DL http://cpanmin.us | perl - <span class="nt" style="color: navy;">-l</span> <span class="nv" style="color: teal;">$(CURDIR)</span>/.tmp App::cpanminus <span class="nb" style="color: #0086b3;">local</span>::lib <span class="p">;</span> <span class="se" style="color: #d14;">\</span></span>
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523
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<pre style="margin: 0;">+<span id="LC523" class="line" lang="make"> <span class="nb" style="color: #0086b3;">eval</span> <span class="sb" style="color: #d14;">`</span>perl <span class="nt" style="color: navy;">-I</span> <span class="nv" style="color: teal;">$(CURDIR)</span>/.<span class="idiff left">tmp/lib/perl5 </span><span class="nt" style="color: navy;"><span class="idiff">-Mlocal</span></span><span class="idiff">::lib</span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="nv" style="color: teal;"><span class="idiff">$(CURDIR)</span></span><span class="idiff right">/</span>.tmp<span class="sb" style="color: #d14;">`</span> <span class="p">;</span> <span class="se" style="color: #d14;">\</span></span>
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524
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<pre style="margin: 0;">+<span id="LC524" class="line" lang="make"> <span class="nv" style="color: teal;">$(CURDIR)</span>/.tmp/bin/cpanm <span class="nt" style="color: navy;">--force</span> Math::Random Clone Test::Deep Sys::Info <span class="p">;</span> <span class="se" style="color: #d14;">\</span></span>
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524
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525
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<pre style="margin: 0;"> <span id="LC525" class="line" lang="make"> <span class="k" style="font-weight: 600;">fi</span></span>
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525
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526
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<pre style="margin: 0;"> <span id="LC526" class="line" lang="make"></span>
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526
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527
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<pre style="margin: 0;"> <span id="LC527" class="line" lang="make"><span class="nl">.PHONY</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">static-libs</span></span>
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527
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528
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<pre style="margin: 0;"> <span id="LC528" class="line" lang="make"><span class="nl">static-libs</span><span class="o" style="font-weight: 600;">:</span></span>
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528
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<pre style="margin: 0;">-<span id="LC528" class="line" lang="make"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[[</span> <span class="o" style="font-weight: 600;">!</span> <span class="nt" style="color: navy;">-d</span> <span class="nv" style="color: teal;">$(CURDIR)</span>/.<span class="idiff left">lib </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="idiff"> </span><span class="nt" style="color: navy;"><span class="idiff">-d</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$(CURDIR)</span></span><span class="idiff right">/.inc</span> <span class="o" style="font-weight: 600;">]]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span> <span class="se" style="color: #d14;">\</span></span>
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529
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<pre style="margin: 0;">-<span id="LC529" class="line" lang="make"> <span class="nb" style="color: #0086b3;">mkdir</span> <span class="nv" style="color: teal;"><span class="idiff left">$(CURDIR)</span></span><span class="idiff">/.lib </span><span class="nv" style="color: teal;"><span class="idiff">$(CURDIR)</span></span><span class="idiff right">/.</span>include <span class="p">;</span> <span class="se" style="color: #d14;">\</span></span>
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529
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<pre style="margin: 0;">+<span id="LC529" class="line" lang="make"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[[</span> <span class="o" style="font-weight: 600;">!</span> <span class="nt" style="color: navy;">-d</span> <span class="nv" style="color: teal;">$(CURDIR)</span>/.<span class="idiff left">tmp/lib </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="idiff"> </span><span class="nt" style="color: navy;"><span class="idiff">-d</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$(CURDIR)</span></span><span class="idiff right">/.tmp/include</span> <span class="o" style="font-weight: 600;">]]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC530" class="line" lang="make"> <span class="nb" style="color: #0086b3;">mkdir</span> <span class="nt" style="color: navy;"><span class="idiff left">-p</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$(CURDIR)</span></span><span class="idiff">/.tmp/lib </span><span class="nv" style="color: teal;"><span class="idiff">$(CURDIR)</span></span><span class="idiff right">/.tmp/</span>include <span class="p">;</span> <span class="se" style="color: #d14;">\</span></span>
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530
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531
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<pre style="margin: 0;"> <span id="LC531" class="line" lang="make"> <span class="k" style="font-weight: 600;">fi</span> <span class="p">;</span> <span class="se" style="color: #d14;">\</span></span>
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531
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532
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<pre style="margin: 0;"> <span id="LC532" class="line" lang="make"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[[</span> <span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">uname</span><span class="sb" style="color: #d14;">`</span> <span class="o" style="font-weight: 600;">=</span> <span class="s2" style="color: #d14;">"Darwin"</span> <span class="o" style="font-weight: 600;">]]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span> <span class="se" style="color: #d14;">\</span></span>
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532
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533
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<pre style="margin: 0;"> <span id="LC533" class="line" lang="make"> <span class="nb" style="color: #0086b3;">export </span><span class="nv" style="color: teal;">CFLAGS</span><span class="o" style="font-weight: 600;">=</span><span class="nt" style="color: navy;">-mmacosx-version-min</span><span class="o" style="font-weight: 600;">=</span>10.9 <span class="p">;</span> <span class="se" style="color: #d14;">\</span></span>
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533
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534
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<pre style="margin: 0;"> <span id="LC534" class="line" lang="make"> <span class="nb" style="color: #0086b3;">export </span><span class="nv" style="color: teal;">CXXFLAGS</span><span class="o" style="font-weight: 600;">=</span><span class="nt" style="color: navy;">-mmacosx-version-min</span><span class="o" style="font-weight: 600;">=</span>10.9 <span class="p">;</span> <span class="se" style="color: #d14;">\</span></span>
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534
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535
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<pre style="margin: 0;"> <span id="LC535" class="line" lang="make"> <span class="k" style="font-weight: 600;">fi</span> <span class="p">;</span> <span class="se" style="color: #d14;">\</span></span>
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535
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536
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<pre style="margin: 0;"> <span id="LC536" class="line" lang="make"> <span class="nv" style="color: teal;">DL</span><span class="o" style="font-weight: 600;">=</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">$$</span><span class="o" style="font-weight: 600;">([</span> <span class="sb" style="color: #d14;">`</span>which wget<span class="sb" style="color: #d14;">`</span> <span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"wget --no-check-certificate"</span> <span class="o" style="font-weight: 600;">||</span> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"curl -LOk"</span><span class="o" style="font-weight: 600;">)</span> <span class="p">;</span> <span class="se" style="color: #d14;">\</span></span>
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536
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<pre style="margin: 0;">-<span id="LC536" class="line" lang="make"> <span class="nb" style="color: #0086b3;">cd</span> /tmp <span class="p">;</span> <span class="se" style="color: #d14;">\</span></span>
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537
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<pre style="margin: 0;">+<span id="LC537" class="line" lang="make"> <span class="nb" style="color: #0086b3;">mkdir</span> .tmp <span class="p">;</span> <span class="se" style="color: #d14;">\</span></span>
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538
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<pre style="margin: 0;">+<span id="LC538" class="line" lang="make"> <span class="nb" style="color: #0086b3;">cd</span> .tmp <span class="p">;</span> <span class="se" style="color: #d14;">\</span></span>
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537
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539
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<pre style="margin: 0;"> <span id="LC539" class="line" lang="make"> <span class="nv" style="color: teal;">$$</span>DL https://zlib.net/zlib-1.2.11.tar.gz <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">tar </span>xzf zlib-1.2.11.tar.gz <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">cd </span>zlib-1.2.11 <span class="p">;</span> <span class="se" style="color: #d14;">\</span></span>
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538
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<pre style="margin: 0;">-<span id="LC538" class="line" lang="make"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="o" style="font-weight: 600;">(</span><span class="k" style="font-weight: 600;">if</span> <span class="nv" style="color: teal;">$(MINGW)</span>, mingw32-make <span class="nt" style="color: navy;">-f</span> win32/Makefile.gcc, ./configure <span class="nt" style="color: navy;">--static</span> <span class="o" style="font-weight: 600;">&&</span> make<span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">cp </span>libz.a <span class="nv" style="color: teal;">$(CURDIR)</span>/.<span class="idiff left">lib </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">cp </span></span><span class="idiff">zconf.h zlib.h </span><span class="nv" style="color: teal;"><span class="idiff">$(CURDIR)</span></span><span class="idiff right">/.</span>include <span class="p">;</span> <span class="se" style="color: #d14;">\</span></span>
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540
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<pre style="margin: 0;">+<span id="LC540" class="line" lang="make"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="o" style="font-weight: 600;">(</span><span class="k" style="font-weight: 600;">if</span> <span class="nv" style="color: teal;">$(MINGW)</span>, mingw32-make <span class="nt" style="color: navy;">-f</span> win32/Makefile.gcc, ./configure <span class="nt" style="color: navy;">--static</span> <span class="o" style="font-weight: 600;">&&</span> make<span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">cp </span>libz.a <span class="nv" style="color: teal;">$(CURDIR)</span>/.<span class="idiff left">tmp/lib </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">cp </span></span><span class="idiff">zconf.h zlib.h </span><span class="nv" style="color: teal;"><span class="idiff">$(CURDIR)</span></span><span class="idiff right">/.tmp/</span>include <span class="p">;</span> <span class="se" style="color: #d14;">\</span></span>
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539
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541
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<pre style="margin: 0;"> <span id="LC541" class="line" lang="make"> <span class="nb" style="color: #0086b3;">cd</span> .. <span class="p">;</span> <span class="se" style="color: #d14;">\</span></span>
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540
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542
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<pre style="margin: 0;"> <span id="LC542" class="line" lang="make"> <span class="nv" style="color: teal;">$$</span>DL https://github.com/01org/tbb/archive/2017_U8.tar.gz <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">tar </span>xzf 2017_U8.tar.gz <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">cd </span>tbb-2017_U8<span class="p">;</span> <span class="se" style="color: #d14;">\</span></span>
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541
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<td class="diff-line-num new_line" data-linenumber="543" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
543
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<pre style="margin: 0;"> <span id="LC543" class="line" lang="make"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="o" style="font-weight: 600;">(</span><span class="k" style="font-weight: 600;">if</span> <span class="nv" style="color: teal;">$(MINGW)</span>, mingw32-make <span class="nv" style="color: teal;">compiler</span><span class="o" style="font-weight: 600;">=</span>gcc <span class="nb" style="color: #0086b3;">arch</span><span class="o" style="font-weight: 600;">=</span>ia64 <span class="nv" style="color: teal;">runtime</span><span class="o" style="font-weight: 600;">=</span>mingw, make<span class="o" style="font-weight: 600;">)</span> <span class="nv" style="color: teal;">extra_inc</span><span class="o" style="font-weight: 600;">=</span>big_iron.inc <span class="nt" style="color: navy;">-j4</span> <span class="se" style="color: #d14;">\</span></span>
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542
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<pre style="margin: 0;">-<span id="LC542" class="line" lang="make"> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">cp</span> <span class="nt" style="color: navy;">-r</span> include/tbb <span class="nv" style="color: teal;">$(CURDIR)</span>/.<span class="idiff left">include </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">cp </span></span><span class="idiff">build/</span><span class="k" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff">_release/</span><span class="k" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff">.a </span><span class="nv" style="color: teal;"><span class="idiff">$(CURDIR)</span></span><span class="idiff right">/.</span>lib</span>
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<pre style="margin: 0;">+<span id="LC544" class="line" lang="make"> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">cp</span> <span class="nt" style="color: navy;">-r</span> include/tbb <span class="nv" style="color: teal;">$(CURDIR)</span>/.<span class="idiff left">tmp/include </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">cp </span></span><span class="idiff">build/</span><span class="k" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff">_release/</span><span class="k" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff">.a </span><span class="nv" style="color: teal;"><span class="idiff">$(CURDIR)</span></span><span class="idiff right">/.tmp/</span>lib</span>
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<pre style="margin: 0;"> <span id="LC545" class="line" lang="make"></span>
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<pre style="margin: 0;"> <span id="LC546" class="line" lang="make"><span class="nl">.PHONY</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">test</span></span>
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<pre style="margin: 0;"> <span id="LC547" class="line" lang="make"><span class="nl">test</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">simple-test random-test</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">@@ -548,8 +550,7 @@ test: simple-test random-test</td>
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<pre style="margin: 0;"> <span id="LC550" class="line" lang="make"><span class="nl">clean</span><span class="o" style="font-weight: 600;">:</span></span>
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551
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<pre style="margin: 0;"> <span id="LC551" class="line" lang="make"> <span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: navy;">-f</span> <span class="nv" style="color: teal;">$(BOWTIE2_BIN_LIST)</span> <span class="nv" style="color: teal;">$(BOWTIE2_BIN_LIST_DBG)</span> <span class="nv" style="color: teal;">$(BOWTIE2_BIN_LIST_SAN)</span> <span class="se" style="color: #d14;">\</span></span>
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550
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552
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<pre style="margin: 0;"> <span id="LC552" class="line" lang="make"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="o" style="font-weight: 600;">(</span>addsuffix .exe,<span class="nv" style="color: teal;">$(BOWTIE2_BIN_LIST)</span> <span class="nv" style="color: teal;">$(BOWTIE2_BIN_LIST_DBG)</span><span class="o" style="font-weight: 600;">)</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">-<span id="LC551" class="line" lang="make"> bowtie2-<span class="idiff left right">src.zip bowtie2-bin</span>.zip</span>
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<pre style="margin: 0;">+<span id="LC553" class="line" lang="make"> bowtie2-<span class="k" style="font-weight: 600;"><span class="idiff left right">*</span></span>.zip</span>
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552
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<pre style="margin: 0;"> <span id="LC554" class="line" lang="make"> <span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: navy;">-f</span> core.<span class="k" style="font-weight: 600;">*</span> .tmp.head</span>
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<pre style="margin: 0;"> <span id="LC555" class="line" lang="make"> <span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: navy;">-rf</span> <span class="k" style="font-weight: 600;">*</span>.dSYM</span>
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<pre style="margin: 0;">-<span id="LC554" class="line" lang="make"> <span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: navy;">-rf</span> .perllib.tmp</span>
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<pre style="margin: 0;">-<span id="LC555" class="line" lang="make"> <span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: navy;">-rf</span> .include .lib</span></pre>
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<pre style="margin: 0;">+<span id="LC556" class="line" lang="make"> <span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: navy;">-rf</span> .tmp</span></pre>
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<li id="9f621eb5fd3bcb2fa5c7bd228c9b1ad42edc46c8">
<a href="https://salsa.debian.org/med-team/bowtie2/commit/157dbc209f47672a9a7167d16e3a324803906000#9f621eb5fd3bcb2fa5c7bd228c9b1ad42edc46c8"><strong>NEWS</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">@@ -19,10 +19,39 @@ Please report any issues to the Bowtie 2 Github page or using the Sourceforge bu</td>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext">Version Release History</span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext">=======================</span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">Version 2.3.4.2 - Aug 7, 2018</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"> * Fixed issue causing `bowtie2` to fail in `--fast-local` mode.</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext"> * Fixed issue causing `--soft-clipped-unmapped-tlen` to be a positional argument.</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext"> * New option `--trim-to N` causes `bowtie2` to trim reads longer</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext"> than `N` bases to exactly `N` bases. Can trim from either 3'</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext"> or 5' end, e.g. `--trim-to 5:30` trims reads to 30 bases,</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext"> truncating at the 5' end.</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext"> * Updated "Building from source" manual section with additional</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext"> instructions on installing TBB.</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext"> * Several other updates to manual, including new mentions of</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext"> [Bioconda](http://bioconda.github.io) and</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext"> [Biocontainers](https://biocontainers.pro).</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext"> * Fixed an issue preventing `bowtie2` from processing more than</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext"> one pattern source when running single threaded.</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext"> * Fixed an issue causing `bowtie2` and `bowtie2-inspect` to crash if</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext"> the index contains a gap-only segment.</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext"> * Added experimental BAM input mode `-b`. Works only with unpaired</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext"> input reads and BAM files that are sorted by read name (`samtools</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext"> sort -n`). BAM input mode also supports the following options:</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext"> o `--preserve-sam-tags`: Preserve any optional fields present in BAM record</span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext"> o `--align-paired-reads`: Paired-end mode for BAM files</span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext"> * Added experimental cmake support</span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext">Thread-scaling paper appears - July 19, 2018</span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext"> * Our latest work on Bowtie's core thread scaling capabilities</span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext"> [just appeared Open Access in the journal Bioinformatics](href="https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/bty648/5055585)</span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="plaintext">Version 2.3.4.1 - Feb 3, 2018</span>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="plaintext"> * Fixed an issue with `--reorder` that caused bowtie2 to crash</span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="plaintext"> while reordering SAM output</span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext"> <span class="idiff left right"> </span>while reordering SAM output</span>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="plaintext">Version 2.3.4 - Dec 29, 2017</span>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">2.3.4.<span class="idiff left right">1</span></span></pre>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">2.3.4.<span class="idiff left right">2</span></span></pre>
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<a href="https://salsa.debian.org/med-team/bowtie2/commit/157dbc209f47672a9a7167d16e3a324803906000#057e0784d807c7b84958635ddeeb5003f2751ece"><strong>aln_sink.cpp</strong></a>
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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>
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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">@@ -2110,6 +2110,7 @@ void AlnSinkSam::appendMate(</td>
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<pre style="margin: 0;"> <span id="LC2110" class="line" lang="cpp"> <span class="n" style="color: #333;">prm</span><span class="p">,</span> <span class="c1" style="color: #998; font-style: italic;">// per-read metrics</span></span>
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<pre style="margin: 0;"> <span id="LC2111" class="line" lang="cpp"> <span class="n" style="color: #333;">sc</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// scoring scheme</span></span>
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<pre style="margin: 0;"> <span id="LC2112" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC2113" class="line" lang="cpp"> <span class="n" style="color: #333;">samc_</span><span class="p">.</span><span class="n" style="color: #333;">printPreservedOptFlags</span><span class="p">(</span><span class="n" style="color: #333;">o</span><span class="p">,</span> <span class="n" style="color: #333;">rd</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC2114" class="line" lang="cpp"> <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="sc" style="color: #d14;">'\n'</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC2115" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC2116" class="line" lang="cpp"></span>
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<a href="https://salsa.debian.org/med-team/bowtie2/commit/157dbc209f47672a9a7167d16e3a324803906000#464ce98392db4e108605b7a12696e7c3434eaf56"><strong>bowtie2-build</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">@@ -80,7 +80,7 @@ def main():</td>
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="python"> <span class="n" style="color: #333;">argv</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">appendleft</span><span class="p">(</span><span class="s" style="color: #d14;">'--wrapper'</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="python"> <span class="n" style="color: #333;">argv</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">appendleft</span><span class="p">(</span><span class="n" style="color: #333;">build_bin_spec</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="python"> <span class="n" style="color: #333;">logging</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">'Command: </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s'</span> <span class="o" style="font-weight: 600;">%</span> <span class="s" style="color: #d14;">' '</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">argv</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC83" class="line" lang="python"> <span class="n" style="color: #333;">s<span class="idiff left">ubprocess</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">call</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff right">argv</span></span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="python"> <span class="n" style="color: #333;">s<span class="idiff left">ys</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">exit</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">subprocess</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">call</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">argv</span></span><span class="p"><span class="idiff right">)</span>)</span></span>
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="python"><span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">__name__</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'__main__'</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="python"> <span class="n" style="color: #333;">main</span><span class="p">()</span></span></pre>
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<a href="https://salsa.debian.org/med-team/bowtie2/commit/157dbc209f47672a9a7167d16e3a324803906000#622d3bcfba0df0e4ae8a0849416ed2d2cf987528"><strong>bowtie2-inspect</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">@@ -77,7 +77,7 @@ def main():</td>
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="python"> <span class="n" style="color: #333;">argv</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">appendleft</span><span class="p">(</span><span class="s" style="color: #d14;">'--wrapper'</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="python"> <span class="n" style="color: #333;">argv</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">appendleft</span><span class="p">(</span><span class="n" style="color: #333;">inspect_bin_spec</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="python"> <span class="n" style="color: #333;">logging</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">'Command: </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s'</span> <span class="o" style="font-weight: 600;">%</span> <span class="s" style="color: #d14;">' '</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">argv</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC80" class="line" lang="python"> <span class="n" style="color: #333;">s<span class="idiff left">ubprocess</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">call</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff right">argv</span></span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="python"> <span class="n" style="color: #333;">s<span class="idiff left">ys</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">exit</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">subprocess</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">call</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">argv</span></span><span class="p"><span class="idiff right">)</span>)</span></span>
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="python"> </span>
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="python"><span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">__name__</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'__main__'</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="python"> <span class="n" style="color: #333;">main</span><span class="p">()</span></span></pre>
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<a href="https://salsa.debian.org/med-team/bowtie2/commit/157dbc209f47672a9a7167d16e3a324803906000#d1904db8401bf0137951f60c3d4a34a7cf8e2e84"><strong>bt2_idx.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">@@ -2530,6 +2530,9 @@ TStr Ebwt::join(EList<FileBuf*>& l,</td>
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<pre style="margin: 0;"> <span id="LC2530" class="line" lang="c"> <span class="k" style="font-weight: 600;">while</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;">i</span><span class="p">]</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">eof</span><span class="p">())</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC2531" class="line" lang="c"> <span class="n" style="color: #333;">RefRecord</span> <span class="n" style="color: #333;">rec</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fastaRefReadAppend</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;">i</span><span class="p">],</span> <span class="n" style="color: #333;">first</span><span class="p">,</span> <span class="n" style="color: #333;">ret</span><span class="p">,</span> <span class="n" style="color: #333;">dstoff</span><span class="p">,</span> <span class="n" style="color: #333;">rpcp</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC2532" class="line" lang="c"> <span class="n" style="color: #333;">first</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="LC2533" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">rec</span><span class="p">.</span><span class="n" style="color: #333;">first</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">rec</span><span class="p">.</span><span class="n" style="color: #333;">len</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="LC2534" class="line" lang="c"> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC2535" class="line" lang="c"> <span class="p">}</span></span>
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2533
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2536
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<pre style="margin: 0;"> <span id="LC2536" class="line" lang="c"> <span class="n" style="color: #333;">TIndexOffU</span> <span class="n" style="color: #333;">bases</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rec</span><span class="p">.</span><span class="n" style="color: #333;">len</span><span class="p">;</span></span>
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2534
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2537
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<pre style="margin: 0;"> <span id="LC2537" class="line" lang="c"> <span class="n" style="color: #333;">assert_eq</span><span class="p">(</span><span class="n" style="color: #333;">rec</span><span class="p">.</span><span class="n" style="color: #333;">off</span><span class="p">,</span> <span class="n" style="color: #333;">szs</span><span class="p">[</span><span class="n" style="color: #333;">szsi</span><span class="p">].</span><span class="n" style="color: #333;">off</span><span class="p">);</span></span>
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2535
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2538
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<pre style="margin: 0;"> <span id="LC2538" class="line" lang="c"> <span class="n" style="color: #333;">assert_eq</span><span class="p">(</span><span class="n" style="color: #333;">rec</span><span class="p">.</span><span class="n" style="color: #333;">len</span><span class="p">,</span> <span class="n" style="color: #333;">szs</span><span class="p">[</span><span class="n" style="color: #333;">szsi</span><span class="p">].</span><span class="n" style="color: #333;">len</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2599" style="width: 35px; color: rgba(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">@@ -2596,7 +2599,7 @@ void Ebwt::joinToDisk(</td>
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2596
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2599
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<pre style="margin: 0;"> <span id="LC2599" class="line" lang="c"> <span class="n" style="color: #333;">writeU</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">TIndexOffU</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="n" style="color: #333;">out1</span><span class="p">,</span> <span class="n" style="color: #333;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">plen</span><span class="p">()[</span><span class="n" style="color: #333;">npat</span><span class="p">],</span> <span class="n" style="color: #333;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">toBe</span><span class="p">());</span></span>
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2597
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2600
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<pre style="margin: 0;"> <span id="LC2600" class="line" lang="c"> <span class="p">}</span></span>
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2598
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2601
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<pre style="margin: 0;"> <span id="LC2601" class="line" lang="c"> <span class="n" style="color: #333;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">plen</span><span class="p">()[</span><span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">npat</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">szs</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">szs</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">off</span><span class="p">);</span></span>
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2599
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<pre style="margin: 0;">-<span id="LC2599" 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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2602
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<pre style="margin: 0;">+<span id="LC2602" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;"><span class="idiff left">if</span></span><span class="p"><span class="idiff">(</span></span><span class="o" style="font-weight: 600;"><span class="idiff">!</span></span><span class="n" style="color: #333;"><span class="idiff">szs</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="p"><span class="idiff">].</span></span><span class="n" style="color: #333;"><span class="idiff">first</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff right"> </span><span class="p">{</span></span>
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2600
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2603
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<pre style="margin: 0;"> <span id="LC2603" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// edge case, but we could get here with npat == -1</span></span>
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2601
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2604
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<pre style="margin: 0;"> <span id="LC2604" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// e.g. when building from a reference of all Ns</span></span>
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2602
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2605
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<pre style="margin: 0;"> <span id="LC2605" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">npat</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;">npat</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="2639" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2642" style="width: 35px; color: rgba(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">@@ -2639,6 +2642,9 @@ void Ebwt::joinToDisk(</td>
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2639
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2642
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<pre style="margin: 0;"> <span id="LC2642" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">//assert_eq(0, _refnames.back().length());</span></span>
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2640
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2643
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<pre style="margin: 0;"> <span id="LC2643" class="line" lang="c"> <span class="n" style="color: #333;">_refnames</span><span class="p">.</span><span class="n" style="color: #333;">pop_back</span><span class="p">();</span></span>
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2641
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2644
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<pre style="margin: 0;"> <span id="LC2644" class="line" lang="c"> <span class="p">}</span></span>
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2645
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<pre style="margin: 0;">+<span id="LC2645" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">rec</span><span class="p">.</span><span class="n" style="color: #333;">first</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">rec</span><span class="p">.</span><span class="n" style="color: #333;">len</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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2646
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<pre style="margin: 0;">+<span id="LC2646" class="line" lang="c"> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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2647
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<pre style="margin: 0;">+<span id="LC2647" class="line" lang="c"> <span class="p">}</span></span>
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2642
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2648
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<pre style="margin: 0;"> <span id="LC2648" class="line" lang="c"> <span class="n" style="color: #333;">assert_lt</span><span class="p">(</span><span class="n" style="color: #333;">szsi</span><span class="p">,</span> <span class="n" style="color: #333;">szs</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">());</span></span>
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2643
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2649
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<pre style="margin: 0;"> <span id="LC2649" class="line" lang="c"> <span class="n" style="color: #333;">assert_eq</span><span class="p">(</span><span class="n" style="color: #333;">rec</span><span class="p">.</span><span class="n" style="color: #333;">off</span><span class="p">,</span> <span class="n" style="color: #333;">szs</span><span class="p">[</span><span class="n" style="color: #333;">szsi</span><span class="p">].</span><span class="n" style="color: #333;">off</span><span class="p">);</span></span>
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2644
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2650
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<pre style="margin: 0;"> <span id="LC2650" class="line" lang="c"> <span class="n" style="color: #333;">assert_eq</span><span class="p">(</span><span class="n" style="color: #333;">rec</span><span class="p">.</span><span class="n" style="color: #333;">len</span><span class="p">,</span> <span class="n" style="color: #333;">szs</span><span class="p">[</span><span class="n" style="color: #333;">szsi</span><span class="p">].</span><span class="n" style="color: #333;">len</span><span class="p">);</span></span>
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<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">@@ -2646,7 +2652,7 @@ void Ebwt::joinToDisk(</td>
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2646
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2652
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<pre style="margin: 0;"> <span id="LC2652" class="line" lang="c"> <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">rec</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;">rec</span><span class="p">.</span><span class="n" style="color: #333;">off</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="2647" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2647
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2653
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<pre style="margin: 0;"> <span id="LC2653" class="line" lang="c"> <span class="n" style="color: #333;">ASSERT_ONLY</span><span class="p">(</span><span class="n" style="color: #333;">szsi</span><span class="o" style="font-weight: 600;">++</span><span class="p">);</span></span>
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2648
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<td class="diff-line-num new_line" data-linenumber="2654" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2654
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<pre style="margin: 0;"> <span id="LC2654" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// Increment seqsRead if this is the first fragment</span></span>
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2649
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<pre style="margin: 0;">-<span id="LC2649" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">rec</span><span class="p">.</span><span class="n" style="color: #333;">first</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">rec</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">len</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="n" style="color: #333;">seqsRead</span><span class="o" style="font-weight: 600;">++</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="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">rec</span><span class="p">.</span><span class="n" style="color: #333;">first</span><span class="p">)</span> <span class="n" style="color: #333;">seqsRead</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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2650
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2656
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<pre style="margin: 0;"> <span id="LC2656" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">bases</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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2651
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2657
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<pre style="margin: 0;"> <span id="LC2657" class="line" lang="c"> <span class="n" style="color: #333;">assert_leq</span><span class="p">(</span><span class="n" style="color: #333;">bases</span><span class="p">,</span> <span class="n" style="color: #333;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">plen</span><span class="p">()[</span><span class="n" style="color: #333;">seqsRead</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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2652
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2658
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<pre style="margin: 0;"> <span id="LC2658" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// Reset the patoff if this is the first fragment</span></span>
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<a href="https://salsa.debian.org/med-team/bowtie2/commit/157dbc209f47672a9a7167d16e3a324803906000#6026283a643bf7fb08c2ef0b797486df93cf0698"><strong>bt2_search.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">@@ -97,6 +97,7 @@ static int ipause; // pause before maching?</td>
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97
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97
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<pre style="margin: 0;"> <span id="LC97" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">qUpto</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// max # of queries to read</span></span>
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98
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98
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<pre style="margin: 0;"> <span id="LC98" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">gTrim5</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// amount to trim from 5' end</span></span>
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99
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99
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">gTrim3</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// amount to trim from 3' end</span></span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</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;">short</span><span class="p">,</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;">trimTo</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// trim reads exceeding given length from either 3' or 5'-end</span></span>
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100
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101
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<pre style="margin: 0;"> <span id="LC101" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">offRate</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// keep default offRate</span></span>
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101
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102
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<pre style="margin: 0;"> <span id="LC102" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">solexaQuals</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// quality strings are solexa quals, not phred, and subtract 64 (not 33)</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="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">phred64Quals</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// quality chars are phred, but must subtract 64 (not 33)</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">@@ -176,6 +177,8 @@ static bool sam_print_zi;</td>
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176
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177
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<pre style="margin: 0;"> <span id="LC177" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">sam_print_zp</span><span class="p">;</span></span>
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177
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178
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<pre style="margin: 0;"> <span id="LC178" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">sam_print_zu</span><span class="p">;</span></span>
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178
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179
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<pre style="margin: 0;"> <span id="LC179" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">sam_print_zt</span><span class="p">;</span></span>
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180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">preserve_sam_tags</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// Only applies when aligning BAM files</span></span>
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<td class="diff-line-num new new_line" data-linenumber="181" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">align_paired_reads</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// Process only the paired reads in BAM file</span></span>
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179
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182
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<pre style="margin: 0;"> <span id="LC182" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">bwaSwLike</span><span class="p">;</span></span>
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180
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183
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<pre style="margin: 0;"> <span id="LC183" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">gSeedLenIsSet</span><span class="p">;</span></span>
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181
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184
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<pre style="margin: 0;"> <span id="LC184" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">bwaSwLikeC</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="288" style="width: 35px; color: rgba(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="291" style="width: 35px; color: rgba(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">@@ -288,6 +291,7 @@ static void resetOptions() {</td>
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288
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291
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<pre style="margin: 0;"> <span id="LC291" class="line" lang="cpp"> <span class="n" style="color: #333;">qUpto</span> <span class="o" style="font-weight: 600;">=</span> <span class="mh" style="color: #099;">0xffffffff</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// max # of queries to read</span></span>
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<pre style="margin: 0;"> <span id="LC292" class="line" lang="cpp"> <span class="n" style="color: #333;">gTrim5</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// amount to trim from 5' end</span></span>
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<pre style="margin: 0;"> <span id="LC293" class="line" lang="cpp"> <span class="n" style="color: #333;">gTrim3</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// amount to trim from 3' end</span></span>
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294
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<pre style="margin: 0;">+<span id="LC294" class="line" lang="cpp"> <span class="n" style="color: #333;">trimTo</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;">short</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="mi" style="color: #099;">5</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;">// default: don't do any trimming</span></span>
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291
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<pre style="margin: 0;"> <span id="LC295" class="line" lang="cpp"> <span class="n" style="color: #333;">offRate</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;">// keep default offRate</span></span>
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292
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296
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<pre style="margin: 0;"> <span id="LC296" class="line" lang="cpp"> <span class="n" style="color: #333;">solexaQuals</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;">// quality strings are solexa quals, not phred, and subtract 64 (not 33)</span></span>
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<td class="diff-line-num old_line" data-linenumber="293" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
293
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<pre style="margin: 0;"> <span id="LC297" class="line" lang="cpp"> <span class="n" style="color: #333;">phred64Quals</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;">// quality chars are phred, but must subtract 64 (not 33)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="369" style="width: 35px; color: rgba(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="373" style="width: 35px; color: rgba(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">@@ -369,6 +373,8 @@ static void resetOptions() {</td>
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369
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<pre style="margin: 0;"> <span id="LC373" class="line" lang="cpp"> <span class="n" style="color: #333;">sam_print_zp</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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370
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<pre style="margin: 0;"> <span id="LC374" class="line" lang="cpp"> <span class="n" style="color: #333;">sam_print_zu</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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371
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<pre style="margin: 0;"> <span id="LC375" class="line" lang="cpp"> <span class="n" style="color: #333;">sam_print_zt</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="LC376" class="line" lang="cpp"> <span class="n" style="color: #333;">preserve_sam_tags</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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377
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<pre style="margin: 0;">+<span id="LC377" class="line" lang="cpp"> <span class="n" style="color: #333;">align_paired_reads</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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372
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378
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<pre style="margin: 0;"> <span id="LC378" class="line" lang="cpp"> <span class="n" style="color: #333;">bwaSwLike</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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373
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379
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<pre style="margin: 0;"> <span id="LC379" class="line" lang="cpp"> <span class="n" style="color: #333;">gSeedLenIsSet</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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374
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380
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<pre style="margin: 0;"> <span id="LC380" class="line" lang="cpp"> <span class="n" style="color: #333;">bwaSwLikeC</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">5.5</span><span class="n" style="color: #333;">f</span><span class="p">;</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -455,7 +461,7 @@ static void resetOptions() {</td>
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461
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<pre style="margin: 0;"> <span id="LC461" class="line" lang="cpp"> <span class="n" style="color: #333;">logDpsOpp</span><span class="p">.</span><span class="n" style="color: #333;">clear</span><span class="p">();</span> <span class="c1" style="color: #998; font-style: italic;">// log mate-search dynamic programming problems</span></span>
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456
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462
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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>
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<pre style="margin: 0;">-<span id="LC458" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</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;">short_options</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"fF:qbzhcu:rv:s:aP:t3:5:w:p:k:M:1:2:I:X:CQ:N:i:L:U:x:S:g:O:D:R:"</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="k" style="font-weight: 600;">static</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;">short_options</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"<span class="idiff left right">b</span>fF:qbzhcu:rv:s:aP:t3:5:w:p:k:M:1:2:I:X:CQ:N:i:L:U:x:S:g:O:D:R:"</span><span class="p">;</span></span>
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465
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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;">static</span> <span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">option</span> <span class="n" style="color: #333;">long_options</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span></span>
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467
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<pre style="margin: 0;"> <span id="LC467" class="line" lang="cpp"><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="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="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">ARG_VERBOSE</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">@@ -643,6 +649,9 @@ static struct option long_options[] = {</td>
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<pre style="margin: 0;"> <span id="LC649" class="line" lang="cpp"><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="s" style="color: #d14;">"xeq"</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="n" style="color: #333;">ARG_XEQ</span><span class="p">},</span></span>
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<pre style="margin: 0;"> <span id="LC650" class="line" lang="cpp"><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="s" style="color: #d14;">"thread-ceiling"</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="n" style="color: #333;">ARG_THREAD_CEILING</span><span class="p">},</span></span>
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<pre style="margin: 0;"> <span id="LC651" class="line" lang="cpp"><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="s" style="color: #d14;">"thread-piddir"</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="n" style="color: #333;">ARG_THREAD_PIDDIR</span><span class="p">},</span></span>
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<pre style="margin: 0;">+<span id="LC652" class="line" lang="cpp"><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="s" style="color: #d14;">"trim-to"</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="n" style="color: #333;">ARG_TRIM_TO</span><span class="p">},</span></span>
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<pre style="margin: 0;">+<span id="LC653" class="line" lang="cpp"><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="s" style="color: #d14;">"preserve-sam-tags"</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="n" style="color: #333;">ARG_PRESERVE_SAM_TAGS</span><span class="p">},</span></span>
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<pre style="margin: 0;">+<span id="LC654" class="line" lang="cpp"><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="s" style="color: #d14;">"align-paired-reads"</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="n" style="color: #333;">ARG_ALIGN_PAIRED_READS</span><span class="p">},</span></span>
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646
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655
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<pre style="margin: 0;"> <span id="LC655" class="line" lang="cpp"><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="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 class="c1" style="color: #998; font-style: italic;">// terminator</span></span>
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647
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656
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<pre style="margin: 0;"> <span id="LC656" class="line" lang="cpp"><span class="p">};</span></span>
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648
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657
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<pre style="margin: 0;"> <span id="LC657" class="line" lang="cpp"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="736" style="width: 35px; color: rgba(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="745" style="width: 35px; color: rgba(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">@@ -736,6 +745,8 @@ static void printUsage(ostream& out) {</td>
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736
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745
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<pre style="margin: 0;"> <span id="LC745" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" -u/--upto <int> stop after first <int> reads/pairs (no limit)"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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737
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<td class="diff-line-num new_line" data-linenumber="746" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
746
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<pre style="margin: 0;"> <span id="LC746" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" -5/--trim5 <int> trim <int> bases from 5'/left end of reads (0)"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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738
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<td class="diff-line-num new_line" data-linenumber="747" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
747
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<pre style="margin: 0;"> <span id="LC747" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" -3/--trim3 <int> trim <int> bases from 3'/right end of reads (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="diff-line-num new new_line" data-linenumber="748" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
748
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<pre style="margin: 0;">+<span id="LC748" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" --trim-to [3:|5:]<int> trim reads exceeding <int> bases from either 3' or 5' end"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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<td class="diff-line-num new new_line" data-linenumber="749" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
749
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<pre style="margin: 0;">+<span id="LC749" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" If the read end is not specified then it defaults to 3 (0)"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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739
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<td class="diff-line-num new_line" data-linenumber="750" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
750
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<pre style="margin: 0;"> <span id="LC750" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" --phred33 qualities are Phred+33 (default)"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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740
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751
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<pre style="margin: 0;"> <span id="LC751" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" --phred64 qualities are Phred+64"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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741
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752
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<pre style="margin: 0;"> <span id="LC752" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" --int-quals qualities encoded as space-delimited integers"</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 old_line" data-linenumber="944" style="width: 35px; color: rgba(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="955" style="width: 35px; color: rgba(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">@@ -944,6 +955,12 @@ static string applyPreset(const string& sorig, Presets& presets) {</td>
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944
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955
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<pre style="margin: 0;"> <span id="LC955" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">saw_M</span><span class="p">;</span></span>
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945
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956
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<pre style="margin: 0;"> <span id="LC956" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">saw_a</span><span class="p">;</span></span>
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946
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957
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<pre style="margin: 0;"> <span id="LC957" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">saw_k</span><span class="p">;</span></span>
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958
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<pre style="margin: 0;">+<span id="LC958" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">saw_trim3</span><span class="p">;</span></span>
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959
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<pre style="margin: 0;">+<span id="LC959" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">saw_trim5</span><span class="p">;</span></span>
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960
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<pre style="margin: 0;">+<span id="LC960" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">saw_trim_to</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="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">saw_bam</span><span class="p">;</span></span>
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962
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<pre style="margin: 0;">+<span id="LC962" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">saw_preserve_sam_tags</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="963" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
963
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<pre style="margin: 0;">+<span id="LC963" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">saw_align_paired_reads</span><span class="p">;</span></span>
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947
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964
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<pre style="margin: 0;"> <span id="LC964" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="n" style="color: #333;">EList</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;">presetList</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="948" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
948
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965
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<pre style="margin: 0;"> <span id="LC965" class="line" lang="cpp"></span>
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<td class="diff-line-num old_line" data-linenumber="949" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
949
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<td class="diff-line-num new_line" data-linenumber="966" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
966
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<pre style="margin: 0;"> <span id="LC966" 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="983" style="width: 35px; color: rgba(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="1000" style="width: 35px; color: rgba(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">@@ -983,6 +1000,11 @@ static void parseOption(int next_option, const char *arg) {</td>
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983
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<td class="diff-line-num new_line" data-linenumber="1000" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1000
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<pre style="margin: 0;"> <span id="LC1000" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">ARG_TAB5</span><span class="p">:</span> <span class="n" style="color: #333;">tokenize</span><span class="p">(</span><span class="n" style="color: #333;">arg</span><span class="p">,</span> <span class="s" style="color: #d14;">","</span><span class="p">,</span> <span class="n" style="color: #333;">mates12</span><span class="p">);</span> <span class="n" style="color: #333;">format</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">TAB_MATE5</span><span class="p">;</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="984" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
984
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<td class="diff-line-num new_line" data-linenumber="1001" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1001
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<pre style="margin: 0;"> <span id="LC1001" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">ARG_TAB6</span><span class="p">:</span> <span class="n" style="color: #333;">tokenize</span><span class="p">(</span><span class="n" style="color: #333;">arg</span><span class="p">,</span> <span class="s" style="color: #d14;">","</span><span class="p">,</span> <span class="n" style="color: #333;">mates12</span><span class="p">);</span> <span class="n" style="color: #333;">format</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">TAB_MATE6</span><span class="p">;</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="985" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
985
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<td class="diff-line-num new_line" data-linenumber="1002" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1002
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<pre style="margin: 0;"> <span id="LC1002" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">ARG_INTERLEAVED_FASTQ</span><span class="p">:</span> <span class="n" style="color: #333;">tokenize</span><span class="p">(</span><span class="n" style="color: #333;">arg</span><span class="p">,</span> <span class="s" style="color: #d14;">","</span><span class="p">,</span> <span class="n" style="color: #333;">mates12</span><span class="p">);</span> <span class="n" style="color: #333;">format</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">INTERLEAVED</span><span class="p">;</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<td class="diff-line-num new old_line" data-linenumber="986" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1003" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1003
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<pre style="margin: 0;">+<span id="LC1003" 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="diff-line-num new new_line" data-linenumber="1004" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1004
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<pre style="margin: 0;">+<span id="LC1004" class="line" lang="cpp"> <span class="n" style="color: #333;">format</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">BAM</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1005" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1005
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<pre style="margin: 0;">+<span id="LC1005" class="line" lang="cpp"> <span class="n" style="color: #333;">saw_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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<td class="diff-line-num new new_line" data-linenumber="1006" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1006
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<pre style="margin: 0;">+<span id="LC1006" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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</td>
<td class="diff-line-num new new_line" data-linenumber="1007" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1007
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<pre style="margin: 0;">+<span id="LC1007" class="line" lang="cpp"> <span class="p">}</span></span>
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986
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<td class="diff-line-num new_line" data-linenumber="1008" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1008
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<pre style="margin: 0;"> <span id="LC1008" 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="n" style="color: #333;">format</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">FASTA</span><span class="p">;</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="987" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
987
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<td class="diff-line-num new_line" data-linenumber="1009" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1009
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<pre style="margin: 0;"> <span id="LC1009" 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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<td class="diff-line-num old_line" data-linenumber="988" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
988
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<td class="diff-line-num new_line" data-linenumber="1010" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1010
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<pre style="margin: 0;"> <span id="LC1010" class="line" lang="cpp"> <span class="n" style="color: #333;">format</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">FASTA_CONT</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1026" style="width: 35px; color: rgba(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="1048" style="width: 35px; color: rgba(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">@@ -1026,6 +1048,16 @@ static void parseOption(int next_option, const char *arg) {</td>
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<td class="diff-line-num old_line" data-linenumber="1026" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1026
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<td class="diff-line-num new_line" data-linenumber="1048" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1048
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<pre style="margin: 0;"> <span id="LC1048" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">ARG_SEED_SUMM</span><span class="p">:</span> <span class="n" style="color: #333;">seedSumm</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="1027" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1027
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<td class="diff-line-num new_line" data-linenumber="1049" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1049
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<pre style="margin: 0;"> <span id="LC1049" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">ARG_SC_UNMAPPED</span><span class="p">:</span> <span class="n" style="color: #333;">scUnMapped</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="1028" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1028
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<td class="diff-line-num new_line" data-linenumber="1050" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1050
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<pre style="margin: 0;"> <span id="LC1050" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">ARG_XEQ</span><span class="p">:</span> <span class="n" style="color: #333;">xeq</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" 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="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">ARG_PRESERVE_SAM_TAGS</span><span class="p">:</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;">preserve_sam_tags</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 new new_line" 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="n" style="color: #333;">saw_preserve_sam_tags</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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1054
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<pre style="margin: 0;">+<span id="LC1054" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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1055
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<pre style="margin: 0;">+<span id="LC1055" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" 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="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">ARG_ALIGN_PAIRED_READS</span><span class="p">:</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1057" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1057
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<pre style="margin: 0;">+<span id="LC1057" class="line" lang="cpp"> <span class="n" style="color: #333;">align_paired_reads</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 new new_line" 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;">saw_align_paired_reads</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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1059
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<pre style="margin: 0;">+<span id="LC1059" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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1060
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<pre style="margin: 0;">+<span id="LC1060" class="line" lang="cpp"> <span class="p">}</span></span>
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1029
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1061
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<pre style="margin: 0;"> <span id="LC1061" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">ARG_MM</span><span class="p">:</span> <span class="p">{</span></span>
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1030
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1062
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<pre style="margin: 0;"> <span id="LC1062" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#ifdef BOWTIE_MM</span></span>
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1031
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1063
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<pre style="margin: 0;"> <span id="LC1063" class="line" lang="cpp"> <span class="n" style="color: #333;">useMm</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="1101" style="width: 35px; color: rgba(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="1133" style="width: 35px; color: rgba(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">@@ -1101,6 +1133,26 @@ static void parseOption(int next_option, const char *arg) {</td>
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1101
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1133
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<pre style="margin: 0;"> <span id="LC1133" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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1102
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<td class="diff-line-num new_line" data-linenumber="1134" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1134
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<pre style="margin: 0;"> <span id="LC1134" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'3'</span><span class="p">:</span> <span class="n" style="color: #333;">gTrim3</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parseInt</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="s" style="color: #d14;">"-3/--trim3 arg must be at least 0"</span><span class="p">,</span> <span class="n" style="color: #333;">arg</span><span class="p">);</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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1103
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<td class="diff-line-num new_line" data-linenumber="1135" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1135
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<pre style="margin: 0;"> <span id="LC1135" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'5'</span><span class="p">:</span> <span class="n" style="color: #333;">gTrim5</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parseInt</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="s" style="color: #d14;">"-5/--trim5 arg must be at least 0"</span><span class="p">,</span> <span class="n" style="color: #333;">arg</span><span class="p">);</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" 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="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">ARG_TRIM_TO</span><span class="p">:</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" 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;">strlen</span><span class="p">(</span><span class="n" style="color: #333;">arg</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;">arg</span><span class="p">[</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;">':'</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" 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;">trimTo</span><span class="p">.</span><span class="n" style="color: #333;">first</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">3</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1139" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1139
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<pre style="margin: 0;">+<span id="LC1139" class="line" lang="cpp"> <span class="n" style="color: #333;">trimTo</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;">parseInt</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="s" style="color: #d14;">"--trim-to: the number of bases to trim must be at least 0"</span><span class="p">,</span> <span class="n" style="color: #333;">arg</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="k" style="font-weight: 600;">break</span><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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<td class="diff-line-num new new_line" data-linenumber="1142" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1142
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<pre style="margin: 0;">+<span id="LC1142" class="line" lang="cpp"> <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="n" style="color: #333;">res</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parsePair</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="n" style="color: #333;">arg</span><span class="p">,</span> <span class="sc" style="color: #d14;">':'</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1143
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<pre style="margin: 0;">+<span id="LC1143" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">res</span><span class="p">.</span><span class="n" style="color: #333;">first</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">3</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">res</span><span class="p">.</span><span class="n" style="color: #333;">first</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">5</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1144" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1144
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<pre style="margin: 0;">+<span id="LC1144" 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;">"--trim-to: trim position must be either 3 or 5"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1145" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1145
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<pre style="margin: 0;">+<span id="LC1145" class="line" lang="cpp"> <span class="n" style="color: #333;">printUsage</span><span class="p">(</span><span class="n" style="color: #333;">cerr</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1146" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1146
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<pre style="margin: 0;">+<span id="LC1146" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">throw</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1147" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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="diff-line-num new new_line" 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;">res</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="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" 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;">"--trim-to: the number bases to trim must be at least 0"</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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1150
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<pre style="margin: 0;">+<span id="LC1150" class="line" lang="cpp"> <span class="n" style="color: #333;">printUsage</span><span class="p">(</span><span class="n" style="color: #333;">cerr</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1151" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1151
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<pre style="margin: 0;">+<span id="LC1151" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">throw</span> <span class="mi" style="color: #099;">1</span><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="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1153" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1153
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<pre style="margin: 0;">+<span id="LC1153" class="line" lang="cpp"> <span class="n" style="color: #333;">trimTo</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">static_cast</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;">short</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</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;">res</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="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1155" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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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1104
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<td class="diff-line-num new_line" data-linenumber="1156" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1156
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<pre style="margin: 0;"> <span id="LC1156" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'h'</span><span class="p">:</span> <span class="n" style="color: #333;">printUsage</span><span class="p">(</span><span class="n" style="color: #333;">cout</span><span class="p">);</span> <span class="k" style="font-weight: 600;">throw</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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1105
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<td class="diff-line-num new_line" data-linenumber="1157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1157
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<pre style="margin: 0;"> <span id="LC1157" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">ARG_USAGE</span><span class="p">:</span> <span class="n" style="color: #333;">printUsage</span><span class="p">(</span><span class="n" style="color: #333;">cout</span><span class="p">);</span> <span class="k" style="font-weight: 600;">throw</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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1106
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<td class="diff-line-num new_line" data-linenumber="1158" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1158
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<pre style="margin: 0;"> <span id="LC1158" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1468" style="width: 35px; color: rgba(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="1520" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1468,12 +1520,6 @@ static void parseOption(int next_option, const char *arg) {</td>
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1468
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1520
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<pre style="margin: 0;"> <span id="LC1520" class="line" lang="cpp"> <span class="n" style="color: #333;">printUsage</span><span class="p">(</span><span class="n" style="color: #333;">cerr</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="1469" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1469
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1521
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<pre style="margin: 0;"> <span id="LC1521" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">throw</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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1470
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<td class="diff-line-num new_line" data-linenumber="1522" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1522
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<pre style="margin: 0;"> <span id="LC1522" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1471" 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">
1471
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<td class="diff-line-num new_line old" data-linenumber="1523" 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="LC1471" 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;">localAlign</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">scUnMapped</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1472" 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">
1472
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<td class="diff-line-num new_line old" data-linenumber="1523" 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="LC1472" class="line" lang="cpp"> <span class="n" style="color: #333;">scUnMapped</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1473" 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">
1473
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<td class="diff-line-num new_line old" data-linenumber="1523" 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="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;">"WARNING: --soft-clipped-unmapped-tlen can only be set for "</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1474" 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">
1474
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<td class="diff-line-num new_line old" data-linenumber="1523" 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="LC1474" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"local alignment... ignoring"</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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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="diff-line-num old old_line" data-linenumber="1476" 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">
1476
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<td class="diff-line-num new_line old" data-linenumber="1523" 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="LC1476" class="line" lang="cpp"></span>
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<td class="diff-line-num old_line" data-linenumber="1477" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1477
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<td class="diff-line-num new_line" data-linenumber="1523" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1523
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<pre style="margin: 0;"> <span id="LC1523" class="line" lang="cpp"><span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="1478" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1478
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<td class="diff-line-num new_line" data-linenumber="1524" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1524
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<pre style="margin: 0;"> <span id="LC1524" class="line" lang="cpp"></span>
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<td class="diff-line-num old_line" data-linenumber="1479" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1479
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<td class="diff-line-num new_line" data-linenumber="1525" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1525
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<pre style="margin: 0;"> <span id="LC1525" 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="1485" style="width: 35px; color: rgba(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="1531" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1485,6 +1531,12 @@ static void parseOptions(int argc, const char **argv) {</td>
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1485
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1531
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<pre style="margin: 0;"> <span id="LC1531" class="line" lang="cpp"> <span class="n" style="color: #333;">saw_M</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="1486" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1486
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<td class="diff-line-num new_line" data-linenumber="1532" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1532
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<pre style="margin: 0;"> <span id="LC1532" class="line" lang="cpp"> <span class="n" style="color: #333;">saw_a</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="1487" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1487
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<td class="diff-line-num new_line" data-linenumber="1533" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1533
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<pre style="margin: 0;"> <span id="LC1533" class="line" lang="cpp"> <span class="n" style="color: #333;">saw_k</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1488" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1534" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1534
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<pre style="margin: 0;">+<span id="LC1534" class="line" lang="cpp"> <span class="n" style="color: #333;">saw_trim3</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1535" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1535
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<pre style="margin: 0;">+<span id="LC1535" class="line" lang="cpp"> <span class="n" style="color: #333;">saw_trim5</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1488" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1536" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1536
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<pre style="margin: 0;">+<span id="LC1536" class="line" lang="cpp"> <span class="n" style="color: #333;">saw_trim_to</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1488" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1537" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1537
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<pre style="margin: 0;">+<span id="LC1537" class="line" lang="cpp"> <span class="n" style="color: #333;">saw_bam</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1538" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1538
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<pre style="margin: 0;">+<span id="LC1538" class="line" lang="cpp"> <span class="n" style="color: #333;">saw_preserve_sam_tags</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1539" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1539
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<pre style="margin: 0;">+<span id="LC1539" class="line" lang="cpp"> <span class="n" style="color: #333;">saw_align_paired_reads</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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<td class="diff-line-num new_line" data-linenumber="1540" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1540
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<pre style="margin: 0;"> <span id="LC1540" class="line" lang="cpp"> <span class="n" style="color: #333;">presetList</span><span class="p">.</span><span class="n" style="color: #333;">clear</span><span class="p">();</span></span>
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1489
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1541
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<pre style="margin: 0;"> <span id="LC1541" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">startVerbose</span><span class="p">)</span> <span class="p">{</span> <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Parsing options: "</span><span class="p">;</span> <span class="n" style="color: #333;">logTime</span><span class="p">(</span><span class="n" style="color: #333;">cerr</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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1490
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<td class="diff-line-num new_line" data-linenumber="1542" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1542
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<pre style="margin: 0;"> <span id="LC1542" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">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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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1503" style="width: 35px; color: rgba(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="1555" style="width: 35px; color: rgba(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">@@ -1503,6 +1555,27 @@ static void parseOptions(int argc, const char **argv) {</td>
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1503
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<td class="diff-line-num new_line" data-linenumber="1555" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1555
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<pre style="margin: 0;"> <span id="LC1555" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="1504" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1504
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<td class="diff-line-num new_line" data-linenumber="1556" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1556
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<pre style="margin: 0;"> <span id="LC1556" class="line" lang="cpp"> <span class="n" style="color: #333;">parseOption</span><span class="p">(</span><span class="n" style="color: #333;">next_option</span><span class="p">,</span> <span class="n" style="color: #333;">arg</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="1505" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1505
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<td class="diff-line-num new_line" data-linenumber="1557" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1557
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<pre style="margin: 0;"> <span id="LC1557" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1558" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1558
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<pre style="margin: 0;">+<span id="LC1558" class="line" lang="cpp"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1559" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1559
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<pre style="margin: 0;">+<span id="LC1559" 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;">localAlign</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">scUnMapped</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1506" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1560" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1560
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<pre style="margin: 0;">+<span id="LC1560" 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: --soft-clipped-unmapped-tlen can only be set for local alignments."</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1561" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1561
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<pre style="margin: 0;">+<span id="LC1561" 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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<td class="diff-line-num new new_line" data-linenumber="1562" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1562
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<pre style="margin: 0;">+<span id="LC1562" class="line" lang="cpp"> <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>
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<td class="diff-line-num new new_line" data-linenumber="1564" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1564
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<pre style="margin: 0;">+<span id="LC1564" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">saw_trim3</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">saw_trim5</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">saw_trim_to</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" 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;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"ERROR: --trim5/--trim3 and --trim-to are mutually exclusive "</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1566" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1566
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<pre style="margin: 0;">+<span id="LC1566" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"options."</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="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="n" style="color: #333;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
</pre>
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<td class="diff-line-num new new_line" 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="p">}</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1569" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1569
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<pre style="margin: 0;">+<span id="LC1569" class="line" lang="cpp"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1570" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1570
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<pre style="margin: 0;">+<span id="LC1570" 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;">saw_bam</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">saw_preserve_sam_tags</span><span class="p">)</span> <span class="p">{</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1571" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1571
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<pre style="margin: 0;">+<span id="LC1571" 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;">"--preserve_sam_tag can only be used when aligning BAM 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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1572
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<pre style="margin: 0;">+<span id="LC1572" 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>
</pre>
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1573
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<pre style="margin: 0;">+<span id="LC1573" class="line" lang="cpp"> <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>
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1575
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<pre style="margin: 0;">+<span id="LC1575" 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;">saw_bam</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">saw_align_paired_reads</span><span class="p">)</span> <span class="p">{</span></span>
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1576
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<pre style="margin: 0;">+<span id="LC1576" 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;">"--align-paired-reads can only be used when aligning BAM 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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1577
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<pre style="margin: 0;">+<span id="LC1577" 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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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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1506
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1579
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<pre style="margin: 0;"> <span id="LC1579" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Now parse all the presets. Might want to pick which presets version to</span></span>
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1507
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1580
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<pre style="margin: 0;"> <span id="LC1580" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// use according to other parameters.</span></span>
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1508
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1581
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<pre style="margin: 0;"> <span id="LC1581" class="line" lang="cpp"> <span class="n" style="color: #333;">auto_ptr</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Presets</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">presets</span><span class="p">(</span><span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">PresetsV0</span><span class="p">());</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4717" style="width: 35px; color: rgba(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="4790" style="width: 35px; color: rgba(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">@@ -4717,11 +4790,14 @@ static void driver(</td>
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4717
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4790
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<pre style="margin: 0;"> <span id="LC4790" class="line" lang="cpp"> <span class="n" style="color: #333;">integerQuals</span><span class="p">,</span> <span class="c1" style="color: #998; font-style: italic;">// true -> qualities are space-separated numbers</span></span>
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<td class="diff-line-num old_line" data-linenumber="4718" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4718
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4791
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<pre style="margin: 0;"> <span id="LC4791" class="line" lang="cpp"> <span class="n" style="color: #333;">gTrim5</span><span class="p">,</span> <span class="c1" style="color: #998; font-style: italic;">// amt to hard clip from 5' end</span></span>
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<td class="diff-line-num old_line" data-linenumber="4719" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4719
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4792
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<pre style="margin: 0;"> <span id="LC4792" class="line" lang="cpp"> <span class="n" style="color: #333;">gTrim3</span><span class="p">,</span> <span class="c1" style="color: #998; font-style: italic;">// amt to hard clip from 3' end</span></span>
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4793
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<pre style="margin: 0;">+<span id="LC4793" class="line" lang="cpp"> <span class="n" style="color: #333;">trimTo</span><span class="p">,</span> <span class="c1" style="color: #998; font-style: italic;">// trim reads exceeding given length from either 3' or 5'-end</span></span>
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4720
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4794
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<pre style="margin: 0;"> <span id="LC4794" class="line" lang="cpp"> <span class="n" style="color: #333;">fastaContLen</span><span class="p">,</span> <span class="c1" style="color: #998; font-style: italic;">// length of sampled reads for FastaContinuous...</span></span>
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4721
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4795
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<pre style="margin: 0;"> <span id="LC4795" class="line" lang="cpp"> <span class="n" style="color: #333;">fastaContFreq</span><span class="p">,</span> <span class="c1" style="color: #998; font-style: italic;">// frequency of sampled reads for FastaContinuous...</span></span>
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4722
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4796
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<pre style="margin: 0;"> <span id="LC4796" class="line" lang="cpp"> <span class="n" style="color: #333;">skipReads</span><span class="p">,</span> <span class="c1" style="color: #998; font-style: italic;">// skip the first 'skip' patterns</span></span>
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4723
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4797
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<pre style="margin: 0;"> <span id="LC4797" class="line" lang="cpp"> <span class="n" style="color: #333;">nthreads</span><span class="p">,</span> <span class="c1" style="color: #998; font-style: italic;">//number of threads for locking</span></span>
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4724
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<pre style="margin: 0;">-<span id="LC4724" class="line" lang="cpp"> <span class="n" style="color: #333;">outType</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">OUTPUT_SAM</span> <span class="c1" style="color: #998; font-style: italic;">// whether to fix mate names</span></span>
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4798
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<pre style="margin: 0;">+<span id="LC4798" class="line" lang="cpp"> <span class="n" style="color: #333;">outType</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">OUTPUT_SAM</span><span class="p">,</span> <span class="c1" style="color: #998; font-style: italic;">// whether to fix mate names</span></span>
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4799
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<pre style="margin: 0;">+<span id="LC4799" class="line" lang="cpp"> <span class="n" style="color: #333;">preserve_sam_tags</span><span class="p">,</span> <span class="c1" style="color: #998; font-style: italic;">// keep existing SAM tags when aligning BAM files</span></span>
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4800
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<pre style="margin: 0;">+<span id="LC4800" class="line" lang="cpp"> <span class="n" style="color: #333;">align_paired_reads</span> <span class="c1" style="color: #998; font-style: italic;">// Align only the paired reads in BAM file</span></span>
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4725
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4801
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<pre style="margin: 0;"> <span id="LC4801" class="line" lang="cpp"> <span class="p">);</span></span>
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4726
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4802
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<pre style="margin: 0;"> <span id="LC4802" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">gVerbose</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">startVerbose</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC4803" 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;">"Creating PatternSource: "</span><span class="p">;</span> <span class="n" style="color: #333;">logTime</span><span class="p">(</span><span class="n" style="color: #333;">cerr</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="html"> <span class="nt" style="color: navy;"><title></span>Bowtie 2 Manual<span class="idiff left right"> – Bowtie 2 Manual</span><span class="nt" style="color: navy;"></title></span></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="html"><span class="nt" style="color: navy;"><nav</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"TOC"</span><span class="nt" style="color: navy;">></span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="html"><span class="nt" style="color: navy;"><ul></span></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="html"><span class="nt" style="color: navy;"><li><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#introduction"</span><span class="nt" style="color: navy;">></span>Introduction<span class="nt" style="color: navy;"></a><ul></span></span>
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27
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="html"><span class="nt" style="color: navy;"><li><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#what-is-bowtie-2"</span><span class="nt" style="color: navy;">></span>What is Bowtie 2?<span class="nt" style="color: navy;"></a></li></span></span>
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28
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="html"><span class="nt" style="color: navy;"><li><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#how-is-bowtie-2-different-from-bowtie-1"</span><span class="nt" style="color: navy;">></span>How is Bowtie 2 different from Bowtie 1?<span class="nt" style="color: navy;"></a></li></span></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="html"><span class="nt" style="color: navy;"><li><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#what-isnt-bowtie-2"</span><span class="nt" style="color: navy;">></span>What isn’t Bowtie 2?<span class="nt" style="color: navy;"></a></li></span></span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="html"><span class="nt" style="color: navy;"><li><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#what-does-it-mean-that-some-older-bowtie-2-versions-are-beta"</span><span class="nt" style="color: navy;">></span>What does it mean that some older Bowtie 2 versions are “beta”?<span class="nt" style="color: navy;"></a></li></span></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="html"><span class="nt" style="color: navy;"></ul></li></span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="html"><span class="nt" style="color: navy;"><li><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#obtaining-bowtie-2"</span><span class="nt" style="color: navy;">></span>Obtaining Bowtie 2<span class="nt" style="color: navy;"></a><ul></span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="html"><span class="nt" style="color: navy;"><li><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#building-from-source"</span><span class="nt" style="color: navy;">></span>Building from source<span class="nt" style="color: navy;"></a></li></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">@@ -105,10 +103,14 @@</td>
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="html"><span class="c" style="color: #998; font-style: italic;"> ! of this text document, or see the HTML manual online.</span></span>
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<pre style="margin: 0;"> <span id="LC104" class="line" lang="html"><span class="c" style="color: #998; font-style: italic;"> ! --></span></span>
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<pre style="margin: 0;"> <span id="LC105" class="line" lang="html"><span class="nt" style="color: navy;"><h1</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"introduction"</span><span class="nt" style="color: navy;">></span>Introduction<span class="nt" style="color: navy;"></h1></span></span>
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<pre style="margin: 0;">-<span id="LC108" class="line" lang="html"><span class="nt" style="color: navy;"><h2</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"what-is-bowtie-2"</span><span class="nt" style="color: navy;">></span>What is Bowtie 2?<span class="nt" style="color: navy;"></h2></span></span>
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<pre style="margin: 0;">-<span id="LC109" class="line" lang="html"><span class="nt" style="color: navy;"><p><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"http://bowtie-bio.sf.net/bowtie2"</span><span class="nt" style="color: navy;">></span>Bowtie 2<span class="nt" style="color: navy;"></a></span> is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with an <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"http://en.wikipedia.org/wiki/FM-index"</span><span class="nt" style="color: navy;">></span>FM Index<span class="nt" style="color: navy;"></a></span> (based on the <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"http://en.wikipedia.org/wiki/Burrows-Wheeler_transform"</span><span class="nt" style="color: navy;">></span>Burrows-Wheeler Transform<span class="nt" style="color: navy;"></a></span> or <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"http://en.wikipedia.org/wiki/Burrows-Wheeler_transform"</span><span class="nt" style="color: navy;">></span>BWT<span class="nt" style="color: navy;"></a></span>) to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 gigabytes of RAM. Bowtie 2 supports gapped, local, and paired-end alignment modes. Multiple processors can be used simultaneously to achieve greater alignment speed. <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"http://cufflinks.cbcb.umd.edu/"</span><span class="nt" style="color: navy;">></span>Cufflinks<span class="nt" style="color: navy;"></a></span>: a tool for transcriptome assembly and isoform quantitiation from Bowtie 2 outputs alignments in <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"http://samtools.sourceforge.net/SAM1.pdf"</span><span class="nt" style="color: navy;">></span>SAM<span class="nt" style="color: navy;"></a></span> format, enabling interoperation with a large number of other tools (e.g. <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"http://samtools.sourceforge.net"</span><span class="nt" style="color: navy;">></span>SAMtools<span class="nt" style="color: navy;"></a></span>, <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"http://www.broadinstitute.org/gsa/wiki/index.php/The_Genome_Analysis_Toolkit"</span><span class="nt" style="color: navy;">></span>GATK<span class="nt" style="color: navy;"></a></span>) that use SAM. Bowtie 2 is distributed under the <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"http://www.gnu.org/licenses/gpl-3.0.html"</span><span class="nt" style="color: navy;">></span>GPLv3 license<span class="nt" style="color: navy;"></a></span>, and it runs on the command line under Windows, Mac OS X and Linux.<span class="nt" style="color: navy;"></p></span></span>
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<pre style="margin: 0;">-<span id="LC110" class="line" lang="html"><span class="nt" style="color: navy;"><p><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"http://bowtie-bio.sf.net/bowtie2"</span><span class="nt" style="color: navy;">></span>Bowtie 2<span class="nt" style="color: navy;"></a></span> is often the first step in pipelines for comparative genomics, including for variation calling, ChIP-seq, RNA-seq, BS-seq. <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"http://bowtie-bio.sf.net/bowtie2"</span><span class="nt" style="color: navy;">></span>Bowtie 2<span class="nt" style="color: navy;"></a></span> and <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"http://bowtie-bio.sf.net"</span><span class="nt" style="color: navy;">></span>Bowtie<span class="nt" style="color: navy;"></a></span> (also called “<span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"http://bowtie-bio.sf.net"</span><span class="nt" style="color: navy;">></span>Bowtie 1<span class="nt" style="color: navy;"></a></span>” here) are also tightly integrated into some tools, including <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"http://tophat.cbcb.umd.edu/"</span><span class="nt" style="color: navy;">></span>TopHat<span class="nt" style="color: navy;"></a></span>: a fast splice junction mapper for RNA-seq reads, RNA-seq reads, <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"http://bowtie-bio.sf.net/crossbow"</span><span class="nt" style="color: navy;">></span>Crossbow<span class="nt" style="color: navy;"></a></span>: a cloud-enabled software tool for analyzing resequencing data, and <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"http://bowtie-bio.sf.net/myrna"</span><span class="nt" style="color: navy;">></span>Myrna<span class="nt" style="color: navy;"></a></span>: a cloud-enabled software tool for aligning RNA-seq reads and measuring differential gene expression.<span class="nt" style="color: navy;"></p></span></span>
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<pre style="margin: 0;">-<span id="LC111" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>If you use <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"http://bowtie-bio.sf.net/bowtie2"</span><span class="nt" style="color: navy;">></span>Bowtie 2<span class="nt" style="color: navy;"></a></span> for your published research, please cite the <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"http://genomebiology.com/2009/10/3/R25"</span><span class="nt" style="color: navy;">></span>Bowtie paper<span class="nt" style="color: navy;"></a></span>. Thank you!<span class="nt" style="color: navy;"></p></span></span>
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<td class="diff-line-num new new_line" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="html"><span class="nt" style="color: navy;"><p><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"http://bowtie-bio.sf.net/bowtie2"</span><span class="nt" style="color: navy;">></span>Bowtie 2<span class="nt" style="color: navy;"></a></span> is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s of characters to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with an <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"http://en.wikipedia.org/wiki/FM-index"</span><span class="nt" style="color: navy;">></span>FM Index<span class="nt" style="color: navy;"></a></span> (based on the <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"http://en.wikipedia.org/wiki/Burrows-Wheeler_transform"</span><span class="nt" style="color: navy;">></span>Burrows-Wheeler Transform<span class="nt" style="color: navy;"></a></span> or <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"http://en.wikipedia.org/wiki/Burrows-Wheeler_transform"</span><span class="nt" style="color: navy;">></span>BWT<span class="nt" style="color: navy;"></a></span>) to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 gigabytes of RAM. Bowtie 2 supports gapped, local, and paired-end alignment modes. Multiple processors can be used simultaneously to achieve greater alignment speed.<span class="nt" style="color: navy;"></p></span></span>
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>Bowtie 2 outputs alignments in <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"http://samtools.sourceforge.net/SAM1.pdf"</span><span class="nt" style="color: navy;">></span>SAM<span class="nt" style="color: navy;"></a></span> format, enabling interoperation with a large number of other tools (e.g. <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"http://samtools.sourceforge.net"</span><span class="nt" style="color: navy;">></span>SAMtools<span class="nt" style="color: navy;"></a></span>, <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"http://www.broadinstitute.org/gsa/wiki/index.php/The_Genome_Analysis_Toolkit"</span><span class="nt" style="color: navy;">></span>GATK<span class="nt" style="color: navy;"></a></span>) that use SAM. Bowtie 2 is distributed under the <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"http://www.gnu.org/licenses/gpl-3.0.html"</span><span class="nt" style="color: navy;">></span>GPLv3 license<span class="nt" style="color: navy;"></a></span>, and it runs on the command line under Windows, Mac OS X and Linux.<span class="nt" style="color: navy;"></p></span></span>
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="html"><span class="nt" style="color: navy;"><p><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"http://bowtie-bio.sf.net/bowtie2"</span><span class="nt" style="color: navy;">></span>Bowtie 2<span class="nt" style="color: navy;"></a></span> is often the first step in pipelines for comparative genomics, including for variation calling, ChIP-seq, RNA-seq, BS-seq. <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"http://bowtie-bio.sf.net/bowtie2"</span><span class="nt" style="color: navy;">></span>Bowtie 2<span class="nt" style="color: navy;"></a></span> and <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"http://bowtie-bio.sf.net"</span><span class="nt" style="color: navy;">></span>Bowtie<span class="nt" style="color: navy;"></a></span> (also called “<span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"http://bowtie-bio.sf.net"</span><span class="nt" style="color: navy;">></span>Bowtie 1<span class="nt" style="color: navy;"></a></span>” here) are also tightly integrated into many other tools, some of which <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"http://bowtie-bio.sourceforge.net/bowtie2/other_tools.shtml"</span><span class="nt" style="color: navy;">></span>are listed here<span class="nt" style="color: navy;"></a></span>.<span class="nt" style="color: navy;"></p></span></span>
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>If you use <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"http://bowtie-bio.sf.net/bowtie2"</span><span class="nt" style="color: navy;">></span>Bowtie 2<span class="nt" style="color: navy;"></a></span> for your published research, please cite our work. Papers describing Bowtie 2 are:<span class="nt" style="color: navy;"></p></span></span>
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="html"><span class="nt" style="color: navy;"><ul></span></span>
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="html"><span class="nt" style="color: navy;"><li><p></span>Langmead B, Wilks C, Antonescu V, Charles R. <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"https://doi.org/10.1093/bioinformatics/bty648"</span><span class="nt" style="color: navy;">></span>Scaling read aligners to hundreds of threads on general-purpose processors<span class="nt" style="color: navy;"></a></span>. <span class="nt" style="color: navy;"><em></span>Bioinformatics<span class="nt" style="color: navy;"></em></span>. 2018 Jul 18. doi: 10.1093/bioinformatics/bty648.<span class="nt" style="color: navy;"></p></li></span></span>
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="html"><span class="nt" style="color: navy;"><li><p></span>Langmead B, Salzberg SL. <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"https://www.nature.com/articles/nmeth.1923"</span><span class="nt" style="color: navy;">></span>Fast gapped-read alignment with Bowtie 2<span class="nt" style="color: navy;"></a></span>. <span class="nt" style="color: navy;"><em></span>Nature Methods<span class="nt" style="color: navy;"></em></span>. 2012 Mar 4;9(4):357-9. doi: 10.1038/nmeth.1923.<span class="nt" style="color: navy;"></p></li></span></span>
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="html"><span class="nt" style="color: navy;"></ul></span></span>
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<pre style="margin: 0;"> <span id="LC114" class="line" lang="html"><span class="nt" style="color: navy;"><h2</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"how-is-bowtie-2-different-from-bowtie-1"</span><span class="nt" style="color: navy;">></span>How is Bowtie 2 different from Bowtie 1?<span class="nt" style="color: navy;"></h2></span></span>
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<pre style="margin: 0;"> <span id="LC115" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>Bowtie 1 was released in 2009 and was geared toward aligning the relatively short sequencing reads (up to 25-50 nucleotides) prevalent at the time. Since then, technology has improved both sequencing throughput (more nucleotides produced per sequencer per day) and read length (more nucleotides per read).<span class="nt" style="color: navy;"></p></span></span>
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<pre style="margin: 0;"> <span id="LC116" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>The chief differences between Bowtie 1 and Bowtie 2 are:<span class="nt" style="color: navy;"></p></span></span>
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<pre style="margin: 0;"> <span id="LC127" class="line" lang="html"><span class="nt" style="color: navy;"></ol></span></span>
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<pre style="margin: 0;"> <span id="LC128" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>Bowtie 2 is not a “drop-in” replacement for Bowtie 1. Bowtie 2’s command-line arguments and genome index format are both different from Bowtie 1’s.<span class="nt" style="color: navy;"></p></span></span>
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<pre style="margin: 0;"> <span id="LC129" class="line" lang="html"><span class="nt" style="color: navy;"><h2</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"what-isnt-bowtie-2"</span><span class="nt" style="color: navy;">></span>What isn’t Bowtie 2?<span class="nt" style="color: navy;"></h2></span></span>
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<pre style="margin: 0;">-<span id="LC128" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>Bowtie 1 and Bowtie 2 are not general-purpose alignment tools like <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"http://mummer.sourceforge.net/"</span><span class="nt" style="color: navy;">></span>MUMmer<span class="nt" style="color: navy;"></a></span>, <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"http://blast.ncbi.nlm.nih.gov/Blast.cgi"</span><span class="nt" style="color: navy;">></span>BLAST<span class="nt" style="color: navy;"></a></span> or <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"http://www.vmatch.de/"</span><span class="nt" style="color: navy;">></span>Vmatch<span class="nt" style="color: navy;"></a></span>. Bowtie 2 works best when aligning to large genomes, though it supports arbitrarily small reference sequences (e.g. amplicons). It handles very long reads (i.e. upwards of 10s or 100s of kilobases), but it is optimized for the read lengths and error modes yielded by recent sequencers, such as the Illumina HiSeq 2000, Roche 454, and Ion Torrent instruments.<span class="nt" style="color: navy;"></p></span></span>
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<pre style="margin: 0;">-<span id="LC129" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>If your goal is to align two very large sequences (e.g. two genomes), consider using <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"http://mummer.sourceforge.net/"</span><span class="nt" style="color: navy;">></span>MUMmer<span class="nt" style="color: navy;"></a></span>. If your goal is very sensitive alignment to a relatively short reference sequence (e.g. a bacterial genome), this can be done with Bowtie 2 but you may want to consider using tools like <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"http://mummer.sourceforge.net/manual/#nucmer"</span><span class="nt" style="color: navy;">></span>NUCmer<span class="nt" style="color: navy;"></a></span>, <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"http://genome.ucsc.edu/cgi-bin/hgBlat?command=start"</span><span class="nt" style="color: navy;">></span>BLAT<span class="nt" style="color: navy;"></a></span>, or <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"http://blast.ncbi.nlm.nih.gov/Blast.cgi"</span><span class="nt" style="color: navy;">></span>BLAST<span class="nt" style="color: navy;"></a></span>. These tools can be extremely slow when the reference genome is long, but are often adequate when the reference is short.<span class="nt" style="color: navy;"></p></span></span>
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<pre style="margin: 0;">-<span id="LC130" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>Bowtie 2 does not support alignment of colorspace reads.<span class="nt" style="color: navy;"></p></span></span>
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<pre style="margin: 0;">-<span id="LC131" class="line" lang="html"><span class="nt" style="color: navy;"><h2</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"what-does-it-mean-that-some-older-bowtie-2-versions-are-beta"</span><span class="nt" style="color: navy;">></span>What does it mean that some older Bowtie 2 versions are “beta”?<span class="nt" style="color: navy;"></h2></span></span>
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<pre style="margin: 0;">-<span id="LC132" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>We said those Bowtie 2 versions were in “beta” to convey that it was not as polished as a tool that had been around for a while, and was still in flux. Since version 2.0.1, we declared Bowtie 2 was no longer “beta”.<span class="nt" style="color: navy;"></p></span></span>
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>Bowtie 2 is geared toward aligning relatively short sequencing reads to long genomes. That said, it handles arbitrarily small reference sequences ( e.g. amplicons) and very long reads (i.e. upwards of 10s or 100s of kilobases), though it is slower in those settings. It is optimized for the read lengths and error modes yielded by typical Illumina sequencers.<span class="nt" style="color: navy;"></p></span></span>
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>Bowtie 2 does not support alignment of colorspace reads. (Bowtie 1 does.)<span class="nt" style="color: navy;"></p></span></span>
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<pre style="margin: 0;"> <span id="LC132" class="line" lang="html"><span class="nt" style="color: navy;"><h1</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"obtaining-bowtie-2"</span><span class="nt" style="color: navy;">></span>Obtaining Bowtie 2<span class="nt" style="color: navy;"></h1></span></span>
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<pre style="margin: 0;">-<span id="LC134" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>Download Bowtie 2 sources and binaries from the <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"https://sourceforge.net/projects/bowtie-bio/files/bowtie2/"</span><span class="nt" style="color: navy;">></span>Download<span class="nt" style="color: navy;"></a></span> section of the Sourceforge site. Binaries are available for the Intel <span class="nt" style="color: navy;"><code></span>x86_64<span class="nt" style="color: navy;"></code></span> architecture running Linux, Mac OS X, and Windows. If you plan to compile Bowtie 2 yourself, make sure to get the source package, i.e., the filename that ends in “-source.zip”.<span class="nt" style="color: navy;"></p></span></span>
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>Bowtie 2 is available from various package managers, notably <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"https://anaconda.org/bioconda/bowtie2"</span><span class="nt" style="color: navy;">></span>Bioconda<span class="nt" style="color: navy;"></a></span>. With Bioconda installed, you should be able to install Bowtie 2 with <span class="nt" style="color: navy;"><code></span>conda install bowtie2<span class="nt" style="color: navy;"></code></span>.<span class="nt" style="color: navy;"></p></span></span>
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>Containerized versions of Bowtie 2 are also available via the <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"https://BioContainers.pro"</span><span class="nt" style="color: navy;">></span>Biocontainers<span class="nt" style="color: navy;"></a></span> project (e.g. <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"https://hub.docker.com/r/biocontainers/bowtie2/"</span><span class="nt" style="color: navy;">></span>via Docker Hub<span class="nt" style="color: navy;"></a></span>).<span class="nt" style="color: navy;"></p></span></span>
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>You can also download Bowtie 2 sources and binaries from the <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"https://sourceforge.net/projects/bowtie-bio/files/bowtie2/"</span><span class="nt" style="color: navy;">></span>Download<span class="nt" style="color: navy;"></a></span> section of the Sourceforge site. Binaries are available for the <span class="nt" style="color: navy;"><code></span>x86_64<span class="nt" style="color: navy;"></code></span> architecture running Linux, Mac OS X, and Windows. If you plan to compile Bowtie 2 yourself, make sure to get the source package, i.e., the filename that ends in “-source.zip”.<span class="nt" style="color: navy;"></p></span></span>
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<pre style="margin: 0;"> <span id="LC136" class="line" lang="html"><span class="nt" style="color: navy;"><h2</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"building-from-source"</span><span class="nt" style="color: navy;">></span>Building from source<span class="nt" style="color: navy;"></h2></span></span>
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<pre style="margin: 0;"> <span id="LC137" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>Building Bowtie 2 from source requires a GNU-like environment with GCC, GNU Make and other basics. It should be possible to build Bowtie 2 on most vanilla Linux installations or on a Mac installation with <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"http://developer.apple.com/xcode/"</span><span class="nt" style="color: navy;">></span>Xcode<span class="nt" style="color: navy;"></a></span> installed. (But see note about the TBB library below). Bowtie 2 can also be built on Windows using a 64-bit MinGW distribution and MSYS. In order to simplify the MinGW setup it might be worth investigating popular MinGW personal builds since these are coming already prepared with most of the toolchains needed.<span class="nt" style="color: navy;"></p></span></span>
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<pre style="margin: 0;"> <span id="LC138" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>First, download the source package from the <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"https://sourceforge.net/projects/bowtie-bio/files/bowtie2/"</span><span class="nt" style="color: navy;">></span>sourceforge site<span class="nt" style="color: navy;"></a></span>. Make sure you’re getting the source package; the file downloaded should end in <span class="nt" style="color: navy;"><code></span>-source.zip<span class="nt" style="color: navy;"></code></span>. Unzip the file, change to the unzipped directory, and build the Bowtie 2 tools by running GNU <span class="nt" style="color: navy;"><code></span>make<span class="nt" style="color: navy;"></code></span> (usually with the command <span class="nt" style="color: navy;"><code></span>make<span class="nt" style="color: navy;"></code></span>, but sometimes with <span class="nt" style="color: navy;"><code></span>gmake<span class="nt" style="color: navy;"></code></span>) with no arguments. If building with MinGW, run <span class="nt" style="color: navy;"><code></span>make<span class="nt" style="color: navy;"></code></span> from the MSYS environment.<span class="nt" style="color: navy;"></p></span></span>
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<pre style="margin: 0;">-<span id="LC138" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>Bowtie 2 can be run on many threads. By default, Bowtie 2 uses the Threading Building Blocks library (TBB) for this. If TBB is not available on your system (e.g. <span class="nt" style="color: navy;"><code></span>make<span class="nt" style="color: navy;"></code></span> prints an error like <span class="nt" style="color: navy;"><code></span>tbb/mutex.h: No such file or directory<span class="nt" style="color: navy;"></code></span>), you can install it yourself (see <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"https://www.threadingbuildingblocks.org"</span><span class="nt" style="color: navy;">></span>Threading Building Blocks library<span class="nt" style="color: navy;"></a></span>) or build Bowtie 2 with <span class="nt" style="color: navy;"><code></span>make NO_TBB=1<span class="nt" style="color: navy;"></code></span> to use pthreads or Windows native multithreading instead.<span class="nt" style="color: navy;"></p></span></span>
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>Bowtie 2 can be run on many threads. By default, Bowtie 2 uses the Threading Building Blocks library (TBB) for this. If TBB is not available on your system (e.g. <span class="nt" style="color: navy;"><code></span>make<span class="nt" style="color: navy;"></code></span> prints an error like <span class="nt" style="color: navy;"><code></span>tbb/mutex.h: No such file or directory<span class="nt" style="color: navy;"></code></span>), you can install it yourself from source (see <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"https://www.threadingbuildingblocks.org"</span><span class="nt" style="color: navy;">></span>Threading Building Blocks library<span class="nt" style="color: navy;"></a></span>) or install it using your operating system’s preferred package manager. The table below list some of the commands for a few of the more popular operating systems.<span class="nt" style="color: navy;"></p></span></span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="html"><span class="nt" style="color: navy;"><table></span></span>
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141
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142
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143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="html">OS</span>
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="html">Sync Package List</span>
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148
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="html">Search</span>
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="html">Install</span>
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156
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="html">Ubuntu, Mint, Debian</span>
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159
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160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="html"><span class="nt" style="color: navy;"><pre><code></span>apt-get update<span class="nt" style="color: navy;"></code></pre></span></span>
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="html"><span class="nt" style="color: navy;"><pre><code></span>apt-cache search tbb<span class="nt" style="color: navy;"></code></pre></span></span>
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164
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165
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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="html"><span class="nt" style="color: navy;"><pre><code></span>apt-get install libtbb-dev<span class="nt" style="color: navy;"></code></pre></span></span>
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167
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168
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169
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170
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171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="html">Fedora, CentOS</span>
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172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="html"><span class="nt" style="color: navy;"></td></span></span>
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173
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174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="html"><span class="nt" style="color: navy;"><pre><code></span>yum check-update<span class="nt" style="color: navy;"></code></pre></span></span>
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175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="html"><span class="nt" style="color: navy;"></td></span></span>
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176
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177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>yum search tbb<span class="nt" style="color: navy;"></p></span></span>
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178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="html"><span class="nt" style="color: navy;"></td></span></span>
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179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="html"><span class="nt" style="color: navy;"><td></span></span>
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180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="html"><span class="nt" style="color: navy;"><pre><code></span>yum install tbb-devel.x86_64<span class="nt" style="color: navy;"></code></pre></span></span>
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181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="html"><span class="nt" style="color: navy;"></td></span></span>
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182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="html"><span class="nt" style="color: navy;"></tr></span></span>
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183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="html"><span class="nt" style="color: navy;"><tr></span></span>
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184
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="html"><span class="nt" style="color: navy;"><td></span></span>
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185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="html">Arch</span>
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186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="html"><span class="nt" style="color: navy;"></td></span></span>
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187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="html"><span class="nt" style="color: navy;"><td></span></span>
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188
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="html"><span class="nt" style="color: navy;"><pre><code></span>packman -Sy<span class="nt" style="color: navy;"></code></pre></span></span>
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189
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190
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191
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="html"><span class="nt" style="color: navy;"><pre><code></span>pacman -Ss tbb<span class="nt" style="color: navy;"></code></pre></span></span>
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192
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193
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194
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="html"><span class="nt" style="color: navy;"><pre><code></span>pacman -S extra/intel-tbb<span class="nt" style="color: navy;"></code></pre></span></span>
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195
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196
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197
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198
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199
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="html">Gentoo</span>
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200
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201
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202
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="html"><span class="nt" style="color: navy;"><pre><code></span>emerge --sync<span class="nt" style="color: navy;"></code></pre></span></span>
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203
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="html"><span class="nt" style="color: navy;"></td></span></span>
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204
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="html"><span class="nt" style="color: navy;"><td></span></span>
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205
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="html"><span class="nt" style="color: navy;"><pre><code></span>emerge --search tbb<span class="nt" style="color: navy;"></code></pre></span></span>
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206
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="html"><span class="nt" style="color: navy;"></td></span></span>
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207
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="html"><span class="nt" style="color: navy;"><td></span></span>
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208
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="html"><span class="nt" style="color: navy;"><pre><code></span>emerge dev-cpp/tbb<span class="nt" style="color: navy;"></code></pre></span></span>
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209
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="html"><span class="nt" style="color: navy;"></td></span></span>
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210
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="html"><span class="nt" style="color: navy;"><tr></span></span>
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211
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="html"><span class="nt" style="color: navy;"><td></span></span>
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212
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="html">MacOS</span>
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="html"><span class="nt" style="color: navy;"><pre><code></span>brew update<span class="nt" style="color: navy;"></code></pre></span></span>
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="html"><span class="nt" style="color: navy;"><pre><code></span>brew search tbb<span class="nt" style="color: navy;"></code></pre></span></span>
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="html"><span class="nt" style="color: navy;"><pre><code></span>brew install tbb<span class="nt" style="color: navy;"></code></pre></span></span>
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="html">FreeBSD</span>
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="html"><span class="nt" style="color: navy;"><pre><code></span>portsnap fetch update<span class="nt" style="color: navy;"></code></pre></span></span>
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230
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231
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<pre style="margin: 0;">+<span id="LC232" class="line" lang="html"><span class="nt" style="color: navy;"><pre><code></span>make search name=tbb<span class="nt" style="color: navy;"></code></pre></span></span>
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233
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234
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="html"><span class="nt" style="color: navy;"><pre><code></span>cd /usr/ports/devel/tbb <span class="ni" style="color: purple;">&&</span> make install <span class="ni" style="color: purple;">&&</span> make clean<span class="nt" style="color: navy;"></code></pre></span></span>
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236
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<pre style="margin: 0;">+<span id="LC236" class="line" lang="html"><span class="nt" style="color: navy;"></table></span></span>
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>The Bowtie 2 Makefile also includes recipes for basic automatic dependency management. Running <span class="nt" style="color: navy;"><code></span>make static-libs <span class="ni" style="color: purple;">&&</span> make STATIC_BUILD=1<span class="nt" style="color: navy;"></code></span> will issue a series of commands that will: 1. download TBB and zlib 2. compile them as static libraries 3. link the resulting libraries to the compiled Bowtie 2 binaries<span class="nt" style="color: navy;"></p></span></span>
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>If all fails Bowtie 2 can be built with <span class="nt" style="color: navy;"><code></span>make NO_TBB=1<span class="nt" style="color: navy;"></code></span> to use pthreads or Windows native multithreading instead.<span class="nt" style="color: navy;"></p></span></span>
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<pre style="margin: 0;"> <span id="LC239" class="line" lang="html"><span class="nt" style="color: navy;"><h2</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"adding-to-path"</span><span class="nt" style="color: navy;">></span>Adding to PATH<span class="nt" style="color: navy;"></h2></span></span>
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<pre style="margin: 0;"> <span id="LC240" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>By adding your new Bowtie 2 directory to your <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"http://en.wikipedia.org/wiki/PATH_(variable)"</span><span class="nt" style="color: navy;">></span>PATH environment variable<span class="nt" style="color: navy;"></a></span>, you ensure that whenever you run <span class="nt" style="color: navy;"><code></span>bowtie2<span class="nt" style="color: navy;"></code></span>, <span class="nt" style="color: navy;"><code></span>bowtie2-build<span class="nt" style="color: navy;"></code></span> or <span class="nt" style="color: navy;"><code></span>bowtie2-inspect<span class="nt" style="color: navy;"></code></span> from the command line, you will get the version you just installed without having to specify the entire path. This is recommended for most users. To do this, follow your operating system’s instructions for adding the directory to your <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"http://en.wikipedia.org/wiki/PATH_(variable)"</span><span class="nt" style="color: navy;">></span>PATH<span class="nt" style="color: navy;"></a></span>.<span class="nt" style="color: navy;"></p></span></span>
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<pre style="margin: 0;"> <span id="LC241" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>If you would like to install Bowtie 2 by copying the Bowtie 2 executable files to an existing directory in your <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"http://en.wikipedia.org/wiki/PATH_(variable)"</span><span class="nt" style="color: navy;">></span>PATH<span class="nt" style="color: navy;"></a></span>, make sure that you copy all the executables, including <span class="nt" style="color: navy;"><code></span>bowtie2<span class="nt" style="color: navy;"></code></span>, <span class="nt" style="color: navy;"><code></span>bowtie2-align-s<span class="nt" style="color: navy;"></code></span>, <span class="nt" style="color: navy;"><code></span>bowtie2-align-l<span class="nt" style="color: navy;"></code></span>, <span class="nt" style="color: navy;"><code></span>bowtie2-build<span class="nt" style="color: navy;"></code></span>, <span class="nt" style="color: navy;"><code></span>bowtie2-build-s<span class="nt" style="color: navy;"></code></span>, <span class="nt" style="color: navy;"><code></span>bowtie2-build-l<span class="nt" style="color: navy;"></code></span>, <span class="nt" style="color: navy;"><code></span>bowtie2-inspect<span class="nt" style="color: navy;"></code></span>, <span class="nt" style="color: navy;"><code></span>bowtie2-inspect-s<span class="nt" style="color: navy;"></code></span> and <span class="nt" style="color: navy;"><code></span>bowtie2-inspect-l<span class="nt" style="color: navy;"></code></span>.<span class="nt" style="color: navy;"></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">@@ -465,6 +565,14 @@ Reads are substrings (k-mers) extracted from a FASTA file <code><s></code></td>
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<pre style="margin: 0;"> <span id="LC567" class="line" lang="html"><span class="nt" style="color: navy;"><tr></span></span>
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<pre style="margin: 0;">+<span id="LC568" class="line" lang="html"><span class="nt" style="color: navy;"><td</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"bowtie2-options-trim-to"</span><span class="nt" style="color: navy;">></span></span>
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<pre style="margin: 0;">+<span id="LC569" class="line" lang="html"><span class="nt" style="color: navy;"><pre><code></span>--trim-to [3:|5:]<span class="ni" style="color: purple;"><</span>int<span class="ni" style="color: purple;">></span><span class="nt" style="color: navy;"></code></pre></span></span>
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<pre style="margin: 0;">+<span id="LC572" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>Trim reads exceeding <span class="nt" style="color: navy;"><code></span><span class="ni" style="color: purple;"><</span>int<span class="ni" style="color: purple;">></span><span class="nt" style="color: navy;"></code></span> bases. Bases will be trimmed from either the 3’ (right) or 5’ (left) end of the read. If the read end if not specified, bowtie 2 will default to trimming from the 3’ (right) end of the read. <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#bowtie2-options-trim-to"</span><span class="nt" style="color: navy;">><code></span>--trim-to<span class="nt" style="color: navy;"></code></a></span> and <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#bowtie2-options-3"</span><span class="nt" style="color: navy;">><code></span>-3<span class="nt" style="color: navy;"></code></a></span>/<span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#bowtie2-options-5"</span><span class="nt" style="color: navy;">><code></span>-5<span class="nt" style="color: navy;"></code></a></span> are mutually exclusive.<span class="nt" style="color: navy;"></p></span></span>
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<pre style="margin: 0;"> <span id="LC576" class="line" lang="html"><span class="nt" style="color: navy;"><td</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"bowtie2-options-phred33-quals"</span><span class="nt" style="color: navy;">></span></span>
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<pre style="margin: 0;"> <span id="LC577" class="line" lang="html"><span class="nt" style="color: navy;"><pre><code></span>--phred33<span class="nt" style="color: navy;"></code></pre></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">@@ -969,11 +1077,11 @@ Seed 4 rc: TTATGCATGA</code></pre></td>
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<pre style="margin: 0;">-<span id="LC972" class="line" lang="html"><span class="nt" style="color: navy;"><td</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"bowtie2-options-soft-clipped-unmapped-tlen<span class="idiff left right">-sec-seq</span>"</span><span class="nt" style="color: navy;">></span></span>
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<pre style="margin: 0;">+<span id="LC1080" class="line" lang="html"><span class="nt" style="color: navy;"><td</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"bowtie2-options-soft-clipped-unmapped-tlen"</span><span class="nt" style="color: navy;">></span></span>
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<pre style="margin: 0;"> <span id="LC1081" class="line" lang="html"><span class="nt" style="color: navy;"><pre><code></span>--soft-clipped-unmapped-tlen<span class="nt" style="color: navy;"></code></pre></span></span>
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<pre style="margin: 0;">-<span id="LC976" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>Consider soft-clipped bases unmapped when calculating <span class="nt" style="color: navy;"><code></span>TLEN<span class="nt" style="color: navy;"></code></span>.<span class="nt" style="color: navy;"></p></span></span>
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<pre style="margin: 0;">+<span id="LC1084" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>Consider soft-clipped bases unmapped when calculating <span class="nt" style="color: navy;"><code></span>TLEN<span class="nt" style="color: navy;"></code></span>.<span class="idiff left"> Only available in </span><span class="nt" style="color: navy;"><span class="idiff"><a</span></span><span class="idiff"> </span><span class="na" style="color: teal;"><span class="idiff">href=</span></span><span class="s" style="color: #d14;"><span class="idiff">"#bowtie2-options-local"</span></span><span class="nt" style="color: navy;"><span class="idiff">><code></span></span><span class="idiff">--local</span><span class="nt" style="color: navy;"><span class="idiff"></code></a></span></span><span class="idiff right"> mode.</span><span class="nt" style="color: navy;"></p></span></span>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext"><h1>Table of Contents</h1></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="html"><span class="nt" style="color: navy;"><p></span><span class="ni" style="color: purple;"> </span>Version <span class="nt" style="color: navy;"><b></span>2.3.4.1<span class="nt" style="color: navy;"></b></p></span></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="html"> <span class="nt" style="color: navy;"><title></span>Bowtie 2 Manual - <span class="nt" style="color: navy;"></title></span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"><nav id="TOC"></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext"><ul></span>
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15
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"><li><a href="#introduction">Introduction</a><ul></span>
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16
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="html"><span class="nt" style="color: navy;"><li><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#what-is-bowtie-2"</span><span class="nt" style="color: navy;">></span>What is Bowtie 2?<span class="nt" style="color: navy;"></a></li></span></span>
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17
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"><li><a href="#how-is-bowtie-2-different-from-bowtie-1">How is Bowtie 2 different from Bowtie 1?</a></li></span>
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18
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext"><li><a href="#what-isnt-bowtie-2">What isn’t Bowtie 2?</a></li></span>
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19
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="html"><span class="nt" style="color: navy;"><li><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"#what-does-it-mean-that-some-older-bowtie-2-versions-are-beta"</span><span class="nt" style="color: navy;">></span>What does it mean that some older Bowtie 2 versions are “beta”?<span class="nt" style="color: navy;"></a></li></span></span>
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20
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7
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"></ul></li></span>
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21
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8
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"><li><a href="#obtaining-bowtie-2">Obtaining Bowtie 2</a><ul></span>
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22
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9
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"><li><a href="#building-from-source">Building from source</a></li></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">@@ -87,17 +74,21 @@</td>
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74
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="plaintext"><li><a href="#using-samtoolsbcftools-downstream">Using SAMtools/BCFtools downstream</a></li></span>
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75
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="plaintext"></ul></li></span>
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76
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="plaintext"></ul></span>
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<pre style="margin: 0;">-<span id="LC90" class="line" lang="html"><span class="nt" style="color: navy;"></<span class="idiff left right">di</span>v></span></span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="plaintext"></<span class="idiff left right">na</span>v></span>
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91
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78
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="plaintext"><!--</span>
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92
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79
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="plaintext"> ! This manual is written in "markdown" format and thus contains some</span>
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93
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80
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="plaintext"> ! distracting formatting clutter. See 'MANUAL' for an easier-to-read version</span>
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="plaintext"> ! of this text document, or see the HTML manual online.</span>
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="plaintext"> ! --></span>
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="plaintext"><h1 id="introduction">Introduction</h1></span>
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<pre style="margin: 0;">-<span id="LC97" class="line" lang="html"><span class="nt" style="color: navy;"><h2</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"what-is-bowtie-2"</span><span class="nt" style="color: navy;">></span>What is Bowtie 2?<span class="nt" style="color: navy;"></h2></span></span>
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<pre style="margin: 0;">-<span id="LC98" class="line" lang="html"><span class="nt" style="color: navy;"><p><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"http://bowtie-bio.sf.net/bowtie2"</span><span class="nt" style="color: navy;">></span>Bowtie 2<span class="nt" style="color: navy;"></a></span> is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with an <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"http://en.wikipedia.org/wiki/FM-index"</span><span class="nt" style="color: navy;">></span>FM Index<span class="nt" style="color: navy;"></a></span> (based on the <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"http://en.wikipedia.org/wiki/Burrows-Wheeler_transform"</span><span class="nt" style="color: navy;">></span>Burrows-Wheeler Transform<span class="nt" style="color: navy;"></a></span> or <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"http://en.wikipedia.org/wiki/Burrows-Wheeler_transform"</span><span class="nt" style="color: navy;">></span>BWT<span class="nt" style="color: navy;"></a></span>) to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 gigabytes of RAM. Bowtie 2 supports gapped, local, and paired-end alignment modes. Multiple processors can be used simultaneously to achieve greater alignment speed. <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"http://cufflinks.cbcb.umd.edu/"</span><span class="nt" style="color: navy;">></span>Cufflinks<span class="nt" style="color: navy;"></a></span>: a tool for transcriptome assembly and isoform quantitiation from Bowtie 2 outputs alignments in <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"http://samtools.sourceforge.net/SAM1.pdf"</span><span class="nt" style="color: navy;">></span>SAM<span class="nt" style="color: navy;"></a></span> format, enabling interoperation with a large number of other tools (e.g. <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"http://samtools.sourceforge.net"</span><span class="nt" style="color: navy;">></span>SAMtools<span class="nt" style="color: navy;"></a></span>, <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"http://www.broadinstitute.org/gsa/wiki/index.php/The_Genome_Analysis_Toolkit"</span><span class="nt" style="color: navy;">></span>GATK<span class="nt" style="color: navy;"></a></span>) that use SAM. Bowtie 2 is distributed under the <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"http://www.gnu.org/licenses/gpl-3.0.html"</span><span class="nt" style="color: navy;">></span>GPLv3 license<span class="nt" style="color: navy;"></a></span>, and it runs on the command line under Windows, Mac OS X and Linux.<span class="nt" style="color: navy;"></p></span></span>
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<pre style="margin: 0;">-<span id="LC99" class="line" lang="html"><span class="nt" style="color: navy;"><p><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"http://bowtie-bio.sf.net/bowtie2"</span><span class="nt" style="color: navy;">></span>Bowtie 2<span class="nt" style="color: navy;"></a></span> is often the first step in pipelines for comparative genomics, including for variation calling, ChIP-seq, RNA-seq, BS-seq. <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"http://bowtie-bio.sf.net/bowtie2"</span><span class="nt" style="color: navy;">></span>Bowtie 2<span class="nt" style="color: navy;"></a></span> and <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"http://bowtie-bio.sf.net"</span><span class="nt" style="color: navy;">></span>Bowtie<span class="nt" style="color: navy;"></a></span> (also called “<span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"http://bowtie-bio.sf.net"</span><span class="nt" style="color: navy;">></span>Bowtie 1<span class="nt" style="color: navy;"></a></span>” here) are also tightly integrated into some tools, including <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"http://tophat.cbcb.umd.edu/"</span><span class="nt" style="color: navy;">></span>TopHat<span class="nt" style="color: navy;"></a></span>: a fast splice junction mapper for RNA-seq reads, RNA-seq reads, <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"http://bowtie-bio.sf.net/crossbow"</span><span class="nt" style="color: navy;">></span>Crossbow<span class="nt" style="color: navy;"></a></span>: a cloud-enabled software tool for analyzing resequencing data, and <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"http://bowtie-bio.sf.net/myrna"</span><span class="nt" style="color: navy;">></span>Myrna<span class="nt" style="color: navy;"></a></span>: a cloud-enabled software tool for aligning RNA-seq reads and measuring differential gene expression.<span class="nt" style="color: navy;"></p></span></span>
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<pre style="margin: 0;">-<span id="LC100" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>If you use <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"http://bowtie-bio.sf.net/bowtie2"</span><span class="nt" style="color: navy;">></span>Bowtie 2<span class="nt" style="color: navy;"></a></span> for your published research, please cite the <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"http://genomebiology.com/2009/10/3/R25"</span><span class="nt" style="color: navy;">></span>Bowtie paper<span class="nt" style="color: navy;"></a></span>. Thank you!<span class="nt" style="color: navy;"></p></span></span>
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="plaintext"><p><a href="http://bowtie-bio.sf.net/bowtie2">Bowtie 2</a> is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s of characters to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with an <a href="http://en.wikipedia.org/wiki/FM-index">FM Index</a> (based on the <a href="http://en.wikipedia.org/wiki/Burrows-Wheeler_transform">Burrows-Wheeler Transform</a> or <a href="http://en.wikipedia.org/wiki/Burrows-Wheeler_transform">BWT</a>) to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 gigabytes of RAM. Bowtie 2 supports gapped, local, and paired-end alignment modes. Multiple processors can be used simultaneously to achieve greater alignment speed.</p></span>
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="plaintext"><p>Bowtie 2 outputs alignments in <a href="http://samtools.sourceforge.net/SAM1.pdf">SAM</a> format, enabling interoperation with a large number of other tools (e.g. <a href="http://samtools.sourceforge.net">SAMtools</a>, <a href="http://www.broadinstitute.org/gsa/wiki/index.php/The_Genome_Analysis_Toolkit">GATK</a>) that use SAM. Bowtie 2 is distributed under the <a href="http://www.gnu.org/licenses/gpl-3.0.html">GPLv3 license</a>, and it runs on the command line under Windows, Mac OS X and Linux.</p></span>
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="plaintext"><p><a href="http://bowtie-bio.sf.net/bowtie2">Bowtie 2</a> is often the first step in pipelines for comparative genomics, including for variation calling, ChIP-seq, RNA-seq, BS-seq. <a href="http://bowtie-bio.sf.net/bowtie2">Bowtie 2</a> and <a href="http://bowtie-bio.sf.net">Bowtie</a> (also called “<a href="http://bowtie-bio.sf.net">Bowtie 1</a>” here) are also tightly integrated into many other tools, some of which <a href="http://bowtie-bio.sourceforge.net/bowtie2/other_tools.shtml">are listed here</a>.</p></span>
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="plaintext"><p>If you use <a href="http://bowtie-bio.sf.net/bowtie2">Bowtie 2</a> for your published research, please cite our work. Papers describing Bowtie 2 are:</p></span>
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="plaintext"><ul></span>
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="plaintext"><li><p>Langmead B, Wilks C, Antonescu V, Charles R. <a href="https://doi.org/10.1093/bioinformatics/bty648">Scaling read aligners to hundreds of threads on general-purpose processors</a>. <em>Bioinformatics</em>. 2018 Jul 18. doi: 10.1093/bioinformatics/bty648.</p></li></span>
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="plaintext"><li><p>Langmead B, Salzberg SL. <a href="https://www.nature.com/articles/nmeth.1923">Fast gapped-read alignment with Bowtie 2</a>. <em>Nature Methods</em>. 2012 Mar 4;9(4):357-9. doi: 10.1038/nmeth.1923.</p></li></span>
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="plaintext"></ul></span>
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="plaintext"><h2 id="how-is-bowtie-2-different-from-bowtie-1">How is Bowtie 2 different from Bowtie 1?</h2></span>
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<pre style="margin: 0;"> <span id="LC93" class="line" lang="plaintext"><p>Bowtie 1 was released in 2009 and was geared toward aligning the relatively short sequencing reads (up to 25-50 nucleotides) prevalent at the time. Since then, technology has improved both sequencing throughput (more nucleotides produced per sequencer per day) and read length (more nucleotides per read).</p></span>
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<pre style="margin: 0;"> <span id="LC94" class="line" lang="plaintext"><p>The chief differences between Bowtie 1 and Bowtie 2 are:</p></span>
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<pre style="margin: 0;"> <span id="LC105" class="line" lang="plaintext"></ol></span>
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<pre style="margin: 0;"> <span id="LC106" class="line" lang="plaintext"><p>Bowtie 2 is not a “drop-in” replacement for Bowtie 1. Bowtie 2’s command-line arguments and genome index format are both different from Bowtie 1’s.</p></span>
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<pre style="margin: 0;"> <span id="LC107" class="line" lang="plaintext"><h2 id="what-isnt-bowtie-2">What isn’t Bowtie 2?</h2></span>
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<pre style="margin: 0;">-<span id="LC117" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>Bowtie 1 and Bowtie 2 are not general-purpose alignment tools like <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"http://mummer.sourceforge.net/"</span><span class="nt" style="color: navy;">></span>MUMmer<span class="nt" style="color: navy;"></a></span>, <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"http://blast.ncbi.nlm.nih.gov/Blast.cgi"</span><span class="nt" style="color: navy;">></span>BLAST<span class="nt" style="color: navy;"></a></span> or <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"http://www.vmatch.de/"</span><span class="nt" style="color: navy;">></span>Vmatch<span class="nt" style="color: navy;"></a></span>. Bowtie 2 works best when aligning to large genomes, though it supports arbitrarily small reference sequences (e.g. amplicons). It handles very long reads (i.e. upwards of 10s or 100s of kilobases), but it is optimized for the read lengths and error modes yielded by recent sequencers, such as the Illumina HiSeq 2000, Roche 454, and Ion Torrent instruments.<span class="nt" style="color: navy;"></p></span></span>
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<pre style="margin: 0;">-<span id="LC118" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>If your goal is to align two very large sequences (e.g. two genomes), consider using <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"http://mummer.sourceforge.net/"</span><span class="nt" style="color: navy;">></span>MUMmer<span class="nt" style="color: navy;"></a></span>. If your goal is very sensitive alignment to a relatively short reference sequence (e.g. a bacterial genome), this can be done with Bowtie 2 but you may want to consider using tools like <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"http://mummer.sourceforge.net/manual/#nucmer"</span><span class="nt" style="color: navy;">></span>NUCmer<span class="nt" style="color: navy;"></a></span>, <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"http://genome.ucsc.edu/cgi-bin/hgBlat?command=start"</span><span class="nt" style="color: navy;">></span>BLAT<span class="nt" style="color: navy;"></a></span>, or <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"http://blast.ncbi.nlm.nih.gov/Blast.cgi"</span><span class="nt" style="color: navy;">></span>BLAST<span class="nt" style="color: navy;"></a></span>. These tools can be extremely slow when the reference genome is long, but are often adequate when the reference is short.<span class="nt" style="color: navy;"></p></span></span>
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<pre style="margin: 0;">-<span id="LC119" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>Bowtie 2 does not support alignment of colorspace reads.<span class="nt" style="color: navy;"></p></span></span>
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<pre style="margin: 0;">-<span id="LC120" class="line" lang="html"><span class="nt" style="color: navy;"><h2</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"what-does-it-mean-that-some-older-bowtie-2-versions-are-beta"</span><span class="nt" style="color: navy;">></span>What does it mean that some older Bowtie 2 versions are “beta”?<span class="nt" style="color: navy;"></h2></span></span>
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<pre style="margin: 0;">-<span id="LC121" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>We said those Bowtie 2 versions were in “beta” to convey that it was not as polished as a tool that had been around for a while, and was still in flux. Since version 2.0.1, we declared Bowtie 2 was no longer “beta”.<span class="nt" style="color: navy;"></p></span></span>
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="plaintext"><p>Bowtie 2 is geared toward aligning relatively short sequencing reads to long genomes. That said, it handles arbitrarily small reference sequences ( e.g. amplicons) and very long reads (i.e. upwards of 10s or 100s of kilobases), though it is slower in those settings. It is optimized for the read lengths and error modes yielded by typical Illumina sequencers.</p></span>
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="plaintext"><p>Bowtie 2 does not support alignment of colorspace reads. (Bowtie 1 does.)</p></span>
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<pre style="margin: 0;"> <span id="LC110" class="line" lang="plaintext"><h1 id="obtaining-bowtie-2">Obtaining Bowtie 2</h1></span>
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<pre style="margin: 0;">-<span id="LC123" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>Download Bowtie 2 sources and binaries from the <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"https://sourceforge.net/projects/bowtie-bio/files/bowtie2/"</span><span class="nt" style="color: navy;">></span>Download<span class="nt" style="color: navy;"></a></span> section of the Sourceforge site. Binaries are available for the Intel <span class="nt" style="color: navy;"><code></span>x86_64<span class="nt" style="color: navy;"></code></span> architecture running Linux, Mac OS X, and Windows. If you plan to compile Bowtie 2 yourself, make sure to get the source package, i.e., the filename that ends in “-source.zip”.<span class="nt" style="color: navy;"></p></span></span>
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="plaintext"><p>Bowtie 2 is available from various package managers, notably <a href="https://anaconda.org/bioconda/bowtie2">Bioconda</a>. With Bioconda installed, you should be able to install Bowtie 2 with <code>conda install bowtie2</code>.</p></span>
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="plaintext"><p>Containerized versions of Bowtie 2 are also available via the <a href="https://BioContainers.pro">Biocontainers</a> project (e.g. <a href="https://hub.docker.com/r/biocontainers/bowtie2/">via Docker Hub</a>).</p></span>
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="plaintext"><p>You can also download Bowtie 2 sources and binaries from the <a href="https://sourceforge.net/projects/bowtie-bio/files/bowtie2/">Download</a> section of the Sourceforge site. Binaries are available for the <code>x86_64</code> architecture running Linux, Mac OS X, and Windows. If you plan to compile Bowtie 2 yourself, make sure to get the source package, i.e., the filename that ends in “-source.zip”.</p></span>
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<pre style="margin: 0;"> <span id="LC114" class="line" lang="plaintext"><h2 id="building-from-source">Building from source</h2></span>
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<pre style="margin: 0;">-<span id="LC125" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>Building Bowtie 2 from source requires a GNU-like environment with GCC, GNU Make and other basics. It should be possible to build Bowtie 2 on most vanilla Linux installations or on a Mac installation with <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"http://developer.apple.com/xcode/"</span><span class="nt" style="color: navy;">></span>Xcode<span class="nt" style="color: navy;"></a></span> installed. Bowtie 2 can also be built on Windows using a 64-bit MinGW distribution and MSYS. In order to simplify the MinGW setup it might be worth investigating popular MinGW personal builds since these are coming already prepared with most of the toolchains needed.<span class="nt" style="color: navy;"></p></span></span>
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="plaintext"><p>Building Bowtie 2 from source requires a GNU-like environment with GCC, GNU Make and other basics. It should be possible to build Bowtie 2 on most vanilla Linux installations or on a Mac installation with <a href="http://developer.apple.com/xcode/">Xcode</a> installed. <span class="idiff left right">(But see note about the TBB library below). </span>Bowtie 2 can also be built on Windows using a 64-bit MinGW distribution and MSYS. In order to simplify the MinGW setup it might be worth investigating popular MinGW personal builds since these are coming already prepared with most of the toolchains needed.</p></span>
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<pre style="margin: 0;"> <span id="LC116" class="line" lang="plaintext"><p>First, download the source package from the <a href="https://sourceforge.net/projects/bowtie-bio/files/bowtie2/">sourceforge site</a>. Make sure you’re getting the source package; the file downloaded should end in <code>-source.zip</code>. Unzip the file, change to the unzipped directory, and build the Bowtie 2 tools by running GNU <code>make</code> (usually with the command <code>make</code>, but sometimes with <code>gmake</code>) with no arguments. If building with MinGW, run <code>make</code> from the MSYS environment.</p></span>
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<pre style="margin: 0;">-<span id="LC127" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>Bowtie 2 is using the multithreading software model in order to speed up execution times on SMP architectures where this is possible. The Threading Building Blocks library, TBB, is now the default threading library in Bowtie 2. On POSIX platforms (like Linux, Mac OS, etc.) if TBB is not available the pthread library will be used. Although it is possible to use pthread library on Windows, a non-POSIX platform, due to performance reasons Bowtie 2 will try to use Windows native multithreading if possible. We recommend that you first install the <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">"https://www.threadingbuildingblocks.org"</span><span class="nt" style="color: navy;">></span>Threading Building Blocks library<span class="nt" style="color: navy;"></a></span>, but if unable to do so please specify <span class="nt" style="color: navy;"><code></span>make NO_TBB=1<span class="nt" style="color: navy;"></code></span>. TBB comes installed by default on many popular Linux distros. Please note, packages built without TBB will have <span class="nt" style="color: navy;"><em></span>-legacy<span class="nt" style="color: navy;"></em></span> appended to the name.<span class="nt" style="color: navy;"></p></span></span>
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="plaintext"><p>Bowtie 2 can be run on many threads. By default, Bowtie 2 uses the Threading Building Blocks library (TBB) for this. If TBB is not available on your system (e.g. <code>make</code> prints an error like <code>tbb/mutex.h: No such file or directory</code>), you can install it yourself from source (see <a href="https://www.threadingbuildingblocks.org">Threading Building Blocks library</a>) or install it using your operating system’s preferred package manager. The table below list some of the commands for a few of the more popular operating systems.</p></span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="plaintext"><table></span>
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119
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120
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="plaintext">OS</span>
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123
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="plaintext">Sync Package List</span>
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125
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="plaintext">Search</span>
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="plaintext">Install</span>
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131
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132
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133
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134
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="plaintext">Ubuntu, Mint, Debian</span>
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136
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137
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="plaintext"><pre><code>apt-get update</code></pre></span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="plaintext"></td></span>
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140
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="plaintext"><pre><code>apt-cache search tbb</code></pre></span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="plaintext"></td></span>
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143
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="plaintext"><pre><code>apt-get install libtbb-dev</code></pre></span>
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145
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146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="plaintext"></tr></span>
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147
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148
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="plaintext">Fedora, CentOS</span>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="plaintext"></td></span>
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151
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152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="plaintext"><pre><code>yum check-update</code></pre></span>
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153
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154
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="plaintext"><p>yum search tbb</p></span>
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156
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157
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158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="plaintext"><pre><code>yum install tbb-devel.x86_64</code></pre></span>
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159
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160
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161
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162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="plaintext"><td></span>
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163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="plaintext">Arch</span>
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="plaintext"><pre><code>packman -Sy</code></pre></span>
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167
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168
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="plaintext"><pre><code>pacman -Ss tbb</code></pre></span>
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170
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171
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172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="plaintext"><pre><code>pacman -S extra/intel-tbb</code></pre></span>
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173
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174
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175
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176
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177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="plaintext">Gentoo</span>
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178
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179
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180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="plaintext"><pre><code>emerge --sync</code></pre></span>
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181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="plaintext"></td></span>
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182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="plaintext"><td></span>
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183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="plaintext"><pre><code>emerge --search tbb</code></pre></span>
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184
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="plaintext"></td></span>
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185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="plaintext"><td></span>
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186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="plaintext"><pre><code>emerge dev-cpp/tbb</code></pre></span>
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187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="plaintext"></td></span>
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188
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189
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190
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="plaintext">MacOS</span>
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191
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="plaintext"></td></span>
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192
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193
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="plaintext"><pre><code>brew update</code></pre></span>
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194
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="plaintext"></td></span>
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195
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196
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="plaintext"><pre><code>brew search tbb</code></pre></span>
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197
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="plaintext"></td></span>
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198
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="plaintext"><td></span>
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199
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="plaintext"><pre><code>brew install tbb</code></pre></span>
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200
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="plaintext"></td></span>
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201
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="plaintext"></tr></span>
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202
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203
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204
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="plaintext">FreeBSD</span>
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205
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="plaintext"></td></span>
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206
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="plaintext"><td></span>
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207
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="plaintext"><pre><code>portsnap fetch update</code></pre></span>
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208
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="plaintext"></td></span>
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209
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="plaintext"><td></span>
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210
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="plaintext"><pre><code>make search name=tbb</code></pre></span>
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211
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="plaintext"></td></span>
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212
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="plaintext"><td></span>
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213
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="plaintext"><pre><code>cd /usr/ports/devel/tbb && make install && make clean</code></pre></span>
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214
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="plaintext"></table></span>
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215
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="plaintext"><p>The Bowtie 2 Makefile also includes recipes for basic automatic dependency management. Running <code>make static-libs && make STATIC_BUILD=1</code> will issue a series of commands that will: 1. download TBB and zlib 2. compile them as static libraries 3. link the resulting libraries to the compiled Bowtie 2 binaries</p></span>
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="plaintext"><p>If all fails Bowtie 2 can be built with <code>make NO_TBB=1</code> to use pthreads or Windows native multithreading instead.</p></span>
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<pre style="margin: 0;"> <span id="LC217" class="line" lang="plaintext"><h2 id="adding-to-path">Adding to PATH</h2></span>
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<pre style="margin: 0;"> <span id="LC218" class="line" lang="plaintext"><p>By adding your new Bowtie 2 directory to your <a href="http://en.wikipedia.org/wiki/PATH_(variable)">PATH environment variable</a>, you ensure that whenever you run <code>bowtie2</code>, <code>bowtie2-build</code> or <code>bowtie2-inspect</code> from the command line, you will get the version you just installed without having to specify the entire path. This is recommended for most users. To do this, follow your operating system’s instructions for adding the directory to your <a href="http://en.wikipedia.org/wiki/PATH_(variable)">PATH</a>.</p></span>
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<pre style="margin: 0;"> <span id="LC219" class="line" lang="plaintext"><p>If you would like to install Bowtie 2 by copying the Bowtie 2 executable files to an existing directory in your <a href="http://en.wikipedia.org/wiki/PATH_(variable)">PATH</a>, make sure that you copy all the executables, including <code>bowtie2</code>, <code>bowtie2-align-s</code>, <code>bowtie2-align-l</code>, <code>bowtie2-build</code>, <code>bowtie2-build-s</code>, <code>bowtie2-build-l</code>, <code>bowtie2-inspect</code>, <code>bowtie2-inspect-s</code> and <code>bowtie2-inspect-l</code>.</p></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">@@ -454,6 +543,14 @@ Reads are substrings (k-mers) extracted from a FASTA file <code><s></code></td>
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<pre style="margin: 0;">+<span id="LC546" class="line" lang="plaintext"><td id="bowtie2-options-trim-to"></span>
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<pre style="margin: 0;">+<span id="LC547" class="line" lang="plaintext"><pre><code>--trim-to [3:|5:]<int></code></pre></span>
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<pre style="margin: 0;">+<span id="LC550" class="line" lang="plaintext"><p>Trim reads exceeding <code><int></code> bases. Bases will be trimmed from either the 3’ (right) or 5’ (left) end of the read. If the read end if not specified, bowtie 2 will default to trimming from the 3’ (right) end of the read. <a href="#bowtie2-options-trim-to"><code>--trim-to</code></a> and <a href="#bowtie2-options-3"><code>-3</code></a>/<a href="#bowtie2-options-5"><code>-5</code></a> are mutually exclusive.</p></span>
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<pre style="margin: 0;"> <span id="LC554" class="line" lang="plaintext"><td id="bowtie2-options-phred33-quals"></span>
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<pre style="margin: 0;"> <span id="LC555" class="line" lang="plaintext"><pre><code>--phred33</code></pre></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">@@ -958,11 +1055,11 @@ Seed 4 rc: TTATGCATGA</code></pre></td>
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<pre style="margin: 0;">-<span id="LC961" class="line" lang="html"><span class="nt" style="color: navy;"><td</span> <span class="na" style="color: teal;">id=</span><span class="s" style="color: #d14;">"bowtie2-options-soft-clipped-unmapped-tlen<span class="idiff left right">-sec-seq</span>"</span><span class="nt" style="color: navy;">></span></span>
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<pre style="margin: 0;">+<span id="LC1058" class="line" lang="plaintext"><td id="bowtie2-options-soft-clipped-unmapped-tlen"></span>
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<pre style="margin: 0;"> <span id="LC1059" class="line" lang="plaintext"><pre><code>--soft-clipped-unmapped-tlen</code></pre></span>
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<pre style="margin: 0;">-<span id="LC965" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>Consider soft-clipped bases unmapped when calculating <span class="nt" style="color: navy;"><code></span>TLEN<span class="nt" style="color: navy;"></code></span>.<span class="nt" style="color: navy;"></p></span></span>
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<pre style="margin: 0;">+<span id="LC1062" class="line" lang="plaintext"><p>Consider soft-clipped bases unmapped when calculating <code>TLEN</code>.<span class="idiff left right"> Only available in <a href="#bowtie2-options-local"><code>--local</code></a> mode.</span></p></span>
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<pre style="margin: 0;"> <span id="LC1063" class="line" lang="plaintext"></td></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext"><h2>Version 2.3.4.2 - August 07, 1987</h2></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"><ul></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> <li>Fixed issue causing <code>bowtie2</code> to fail in <code><a href="bowtie2-options-fast-local">--fast-local</a></code> mode.</li></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> <li>Fixed issue causing <code><a href="bowtie2-options-soft-clipped-unmapped-tlen>--soft-clipped-unmapped-tlen</a></code> to be a positional argument.</li></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> <li>New option <code><a href="bowtie2-options-trim-to">--trim-to</a> N</code> causes <code>bowtie2</code> to trim reads longer than <code>N</code> bases to exactly <code>N</code> bases. Can trim from either 3' or 5' end, e.g. <code><a href="bowtie2-options-trim-to">--trim-to</a> 5:30</code> trims reads to 30 bases, truncating at the 5' end.</li></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> <li>Updated <a href="#building-from-source">"Building from source"</a> manual section with additional instructions on installing TBB.</li></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> <li>Several other updates to manual, including new mentions of <a href="http://bioconda.github.io">Bioconda</a> and <a href="https://biocontainers.pro">Biocontainers</a>.</li></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> <li>Fixed an issue preventing <code>bowtie2</code> from processing more than one pattern source when running single threaded.</li></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> <li>Fixed an issue causing <code>bowtie2</code> and <code>bowtie2-inspect</code> to crash if the index contains a gap-only segment.</li></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> <li>Added <i>experimental</i> BAM input mode <code>-b</code>. Works only with unpaired input reads and BAM files that are sorted by read name (<code>samtools sort -n</code>). BAM input mode also supports the following options:<li></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> <ul></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> <li><code>--preserve-sam-tags</code>: Preserve any optional fields present in BAM record</li></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> <li><code>--align-paired-reads</code>: Paired-end mode for BAM files</li></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> </ul></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"> <li>Add <i>experimental</i> CMake support</li></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"><h2>Thread-scaling paper appears - July 19, 2018</h2></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"><ul></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"> <li>Our latest work on Bowtie's core thread scaling capabilities <a href="https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/bty648/5055585">just appeared Open Access in the journal Bioinformatics</a></li></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext"><h2>Version 2.3.4.1 - February 03, 2018</h2></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext"><ul></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext"> <li>Fixed an issue with <tt><a href="manual.shtml#bowtie2-options-reorder">--reorder</a></tt> that caused bowtie2 to crash while reordering SAM output</li></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="plaintext"> <a href="https://sourceforge.net/projects/bowtie-bio/files/bowtie2/2.3.4.<span class="idiff left right">1">Bowtie2 2.3.4.1</span></a></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"> <a href="https://sourceforge.net/projects/bowtie-bio/files/bowtie2/2.3.4.<span class="idiff left right">2">Bowtie2 2.3.4.2</span></a></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="plaintext"> 0<span class="idiff left right">2/03</span>/18 </span>
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<a href="https://salsa.debian.org/med-team/bowtie2/commit/157dbc209f47672a9a7167d16e3a324803906000#f33859afffab10e65cd96fbe0811935a2f3508a1"><strong>example/reads/combined_reads.bam</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">@@ -31,6 +31,7 @@ enum file_format {</td>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="c"> <span class="n" style="color: #333;">FASTA_CONT</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="c"> <span class="n" style="color: #333;">FASTQ</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="c"> <span class="n" style="color: #333;">INTERLEAVED</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="c"> <span class="n" style="color: #333;">BAM</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="c"> <span class="n" style="color: #333;">TAB_MATE5</span><span class="p">,</span></span>
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35
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36
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="c"> <span class="n" style="color: #333;">TAB_MATE6</span><span class="p">,</span></span>
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37
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="c"> <span class="n" style="color: #333;">RAW</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">@@ -43,12 +44,14 @@ static const std::string file_format_names[] = {</td>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="c"> <span class="s" style="color: #d14;">"FASTA"</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="c"> <span class="s" style="color: #d14;">"FASTA sampling"</span><span class="p">,</span></span>
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46
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="c"> <span class="s" style="color: #d14;">"FASTQ"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="c"> <span class="s" style="color: #d14;">"Interleaved FASTQ"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="c"> <span class="s" style="color: #d14;">"BAM"</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="c"> <span class="s" style="color: #d14;">"Tabbed mated"</span><span class="p">,</span></span>
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50
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="c"> <span class="s" style="color: #d14;">"Raw"</span><span class="p">,</span></span>
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51
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="c"> <span class="s" style="color: #d14;">"Command line"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="c"> <span class="s" style="color: #d14;">"Qseq"</span><span class="p">,</span></span>
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53
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="c"> <span class="s" style="color: #d14;">"Chain file"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="c"> <span class="s" style="color: #d14;">"Random"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="c"> <span class="s" style="color: #d14;">"Qseq"</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="c"> <span class="s" style="color: #d14;">"Random"</span></span>
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55
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="c"><span class="p">};</span></span>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif </span><span class="cm" style="color: #998; font-style: italic;">/*FORMATS_H_*/</span></span></pre>
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<a href="https://salsa.debian.org/med-team/bowtie2/commit/157dbc209f47672a9a7167d16e3a324803906000#50b0e95b63ccb2c46e008fda8904d780b714df41"><strong>opts.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">@@ -156,7 +156,10 @@ enum {</td>
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<pre style="margin: 0;"> <span id="LC156" class="line" lang="c"> <span class="n" style="color: #333;">ARG_XEQ</span><span class="p">,</span> <span class="c1" style="color: #998; font-style: italic;">// --xeq</span></span>
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157
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<pre style="margin: 0;"> <span id="LC157" class="line" lang="c"> <span class="n" style="color: #333;">ARG_THREAD_CEILING</span><span class="p">,</span> <span class="c1" style="color: #998; font-style: italic;">// --thread-ceiling</span></span>
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158
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<pre style="margin: 0;"> <span id="LC158" class="line" lang="c"> <span class="n" style="color: #333;">ARG_THREAD_PIDDIR</span><span class="p">,</span> <span class="c1" style="color: #998; font-style: italic;">// --thread-piddir</span></span>
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159
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<pre style="margin: 0;">-<span id="LC159" class="line" lang="c"> <span class="n" style="color: #333;">ARG_INTERLEAVED_FASTQ</span> <span class="c1" style="color: #998; font-style: italic;">// --interleaved</span></span>
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159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="c"> <span class="n" style="color: #333;">ARG_INTERLEAVED_FASTQ</span><span class="p">,</span> <span class="c1" style="color: #998; font-style: italic;">// --interleaved</span></span>
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="c"> <span class="n" style="color: #333;">ARG_TRIM_TO</span><span class="p">,</span> <span class="c1" style="color: #998; font-style: italic;">// --trim-to</span></span>
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="c"> <span class="n" style="color: #333;">ARG_PRESERVE_SAM_TAGS</span><span class="p">,</span> <span class="c1" style="color: #998; font-style: italic;">// --preserve-sam-tags</span></span>
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="c"> <span class="n" style="color: #333;">ARG_ALIGN_PAIRED_READS</span><span class="p">,</span> <span class="c1" style="color: #998; font-style: italic;">// --align-paired-reads</span></span>
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<pre style="margin: 0;"> <span id="LC163" class="line" lang="c"><span class="p">};</span></span>
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<pre style="margin: 0;"> <span id="LC164" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC165" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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<a href="https://salsa.debian.org/med-team/bowtie2/commit/157dbc209f47672a9a7167d16e3a324803906000#7c4ae52e4a13c990d16c9530fb874ed79064a5cd"><strong>pat.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">@@ -18,9 +18,12 @@</td>
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18
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<pre style="margin: 0;"> <span id="LC18" 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="LC19" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <cmath></span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <stdio.h></span></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <iostream></span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <sstream></span></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <string></span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <stdexcept></span></span>
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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 <string.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 "sstring.h"</span></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="cpp"></span>
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26
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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 "pat.h"</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="98" style="width: 35px; color: rgba(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="101" style="width: 35px; color: rgba(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">@@ -98,6 +101,7 @@ PatternSource* PatternSource::patsrcFromStrings(</td>
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98
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101
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<pre style="margin: 0;"> <span id="LC101" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">FASTA_CONT</span><span class="p">:</span> <span class="k" style="font-weight: 600;">return</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">FastaContinuousPatternSource</span><span class="p">(</span><span class="n" style="color: #333;">qs</span><span class="p">,</span> <span class="n" style="color: #333;">p</span><span class="p">);</span></span>
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99
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102
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<pre style="margin: 0;"> <span id="LC102" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">RAW</span><span class="p">:</span> <span class="k" style="font-weight: 600;">return</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">RawPatternSource</span><span class="p">(</span><span class="n" style="color: #333;">qs</span><span class="p">,</span> <span class="n" style="color: #333;">p</span><span class="p">);</span></span>
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100
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103
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">FASTQ</span><span class="p">:</span> <span class="k" style="font-weight: 600;">return</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">FastqPatternSource</span><span class="p">(</span><span class="n" style="color: #333;">qs</span><span class="p">,</span> <span class="n" style="color: #333;">p</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">BAM</span><span class="p">:</span> <span class="k" style="font-weight: 600;">return</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">BAMPatternSource</span><span class="p">(</span><span class="n" style="color: #333;">qs</span><span class="p">,</span> <span class="n" style="color: #333;">p</span><span class="p">);</span></span>
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101
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105
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<pre style="margin: 0;"> <span id="LC105" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">INTERLEAVED</span><span class="p">:</span> <span class="k" style="font-weight: 600;">return</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">FastqPatternSource</span><span class="p">(</span><span class="n" style="color: #333;">qs</span><span class="p">,</span> <span class="n" style="color: #333;">p</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">true</span> <span class="cm" style="color: #998; font-style: italic;">/* interleaved */</span><span class="p">);</span></span>
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102
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106
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<pre style="margin: 0;"> <span id="LC106" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">TAB_MATE5</span><span class="p">:</span> <span class="k" style="font-weight: 600;">return</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">TabbedPatternSource</span><span class="p">(</span><span class="n" style="color: #333;">qs</span><span class="p">,</span> <span class="n" style="color: #333;">p</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">);</span></span>
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103
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107
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<pre style="margin: 0;"> <span id="LC107" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">TAB_MATE6</span><span class="p">:</span> <span class="k" style="font-weight: 600;">return</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">TabbedPatternSource</span><span class="p">(</span><span class="n" style="color: #333;">qs</span><span class="p">,</span> <span class="n" style="color: #333;">p</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="172" style="width: 35px; color: rgba(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="176" style="width: 35px; color: rgba(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">@@ -172,8 +176,11 @@ pair<bool, bool> PatternSourcePerThread::nextReadPair() {</td>
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172
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176
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<pre style="margin: 0;"> <span id="LC176" class="line" lang="cpp"> <span class="p">}</span></span>
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173
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177
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<pre style="margin: 0;"> <span id="LC177" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Finalize read/pair</span></span>
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174
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178
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<pre style="margin: 0;"> <span id="LC178" 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;">buf_</span><span class="p">.</span><span class="n" style="color: #333;">read_b</span><span class="p">().</span><span class="n" style="color: #333;">patFw</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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179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="cpp"> <span class="n" style="color: #333;">trim</span><span class="p">(</span><span class="n" style="color: #333;">buf_</span><span class="p">.</span><span class="n" style="color: #333;">read_a</span><span class="p">());</span></span>
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180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="cpp"> <span class="n" style="color: #333;">trim</span><span class="p">(</span><span class="n" style="color: #333;">buf_</span><span class="p">.</span><span class="n" style="color: #333;">read_b</span><span class="p">());</span></span>
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175
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181
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<pre style="margin: 0;"> <span id="LC181" class="line" lang="cpp"> <span class="n" style="color: #333;">finalizePair</span><span class="p">(</span><span class="n" style="color: #333;">buf_</span><span class="p">.</span><span class="n" style="color: #333;">read_a</span><span class="p">(),</span> <span class="n" style="color: #333;">buf_</span><span class="p">.</span><span class="n" style="color: #333;">read_b</span><span class="p">());</span></span>
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176
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182
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<pre style="margin: 0;"> <span id="LC182" 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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183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="cpp"> <span class="n" style="color: #333;">trim</span><span class="p">(</span><span class="n" style="color: #333;">buf_</span><span class="p">.</span><span class="n" style="color: #333;">read_a</span><span class="p">());</span></span>
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177
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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;">finalize</span><span class="p">(</span><span class="n" style="color: #333;">buf_</span><span class="p">.</span><span class="n" style="color: #333;">read_a</span><span class="p">());</span></span>
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178
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185
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<pre style="margin: 0;"> <span id="LC185" class="line" lang="cpp"> <span class="p">}</span></span>
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179
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<pre style="margin: 0;"> <span id="LC186" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">this_is_last</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">buf_</span><span class="p">.</span><span class="n" style="color: #333;">cur_buf_</span> <span class="o" style="font-weight: 600;">==</span> <span class="k" style="font-weight: 600;">static_cast</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="n" style="color: #333;">last_batch_size_</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">@@ -268,7 +275,7 @@ pair<bool, int> DualPatternComposer::nextBatch(PerThreadReadBuf& pt) {</td>
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268
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275
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<pre style="margin: 0;"> <span id="LC275" class="line" lang="cpp"> <span class="p">}</span></span>
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269
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276
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<pre style="margin: 0;"> <span id="LC276" class="line" lang="cpp"> <span class="n" style="color: #333;">assert_eq</span><span class="p">(</span><span class="n" style="color: #333;">resa</span><span class="p">.</span><span class="n" style="color: #333;">first</span><span class="p">,</span> <span class="n" style="color: #333;">resb</span><span class="p">.</span><span class="n" style="color: #333;">first</span><span class="p">);</span></span>
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270
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277
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<pre style="margin: 0;"> <span id="LC277" class="line" lang="cpp"> <span class="n" style="color: #333;">assert_eq</span><span class="p">(</span><span class="n" style="color: #333;">resa</span><span class="p">.</span><span class="n" style="color: #333;">second</span><span class="p">,</span> <span class="n" style="color: #333;">resb</span><span class="p">.</span><span class="n" style="color: #333;">second</span><span class="p">);</span></span>
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271
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<pre style="margin: 0;">-<span id="LC271" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">make_pair</span><span class="p">(</span><span class="n" style="color: #333;">resa</span><span class="p">.</span><span class="n" style="color: #333;">first</span><span class="p">,</span> <span class="n" style="color: #333;">resa</span><span class="p">.</span><span class="n" style="color: #333;">second</span><span class="p">);</span></span>
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278
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<pre style="margin: 0;">+<span id="LC278" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">make_pair</span><span class="p">(</span><span class="n" style="color: #333;">resa</span><span class="p">.</span><span class="n" style="color: #333;">first</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">cur</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">srca_</span></span><span class="o" style="font-weight: 600;"><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 right">1</span></span><span class="p">,</span> <span class="n" style="color: #333;">resa</span><span class="p">.</span><span class="n" style="color: #333;">second</span><span class="p">);</span></span>
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272
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279
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<pre style="margin: 0;"> <span id="LC279" class="line" lang="cpp"> <span class="p">}</span></span>
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273
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280
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<pre style="margin: 0;"> <span id="LC280" class="line" lang="cpp"> <span class="p">}</span></span>
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274
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281
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<pre style="margin: 0;"> <span id="LC281" class="line" lang="cpp"> <span class="n" style="color: #333;">assert_leq</span><span class="p">(</span><span class="n" style="color: #333;">cur</span><span class="p">,</span> <span class="n" style="color: #333;">srca_</span><span class="o" style="font-weight: 600;">-></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="463" style="width: 35px; color: rgba(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">@@ -463,23 +470,22 @@ void CFilePatternSource::open() {</td>
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463
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470
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<pre style="margin: 0;"> <span id="LC470" class="line" lang="cpp"> <span class="n" style="color: #333;">zfp_</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gzdopen</span><span class="p">(</span><span class="n" style="color: #333;">fn</span><span class="p">,</span> <span class="s" style="color: #d14;">"rb"</span><span class="p">);</span></span>
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464
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471
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<pre style="margin: 0;"> <span id="LC471" class="line" lang="cpp"> <span class="p">}</span></span>
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465
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472
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<pre style="margin: 0;"> <span id="LC472" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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466
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<pre style="margin: 0;">-<span id="LC466" class="line" lang="cpp"> <span class="n" style="color: #333;">compressed_</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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467
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<pre style="margin: 0;">-<span id="LC467" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">is_gzipped_file</span><span class="p">(</span><span class="n" style="color: #333;">infiles_</span><span class="p">[</span><span class="n" style="color: #333;">filecur_</span><span class="p">]))</span> <span class="p">{</span></span>
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468
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<pre style="margin: 0;">-<span id="LC468" class="line" lang="cpp"> <span class="n" style="color: #333;">compressed_</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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469
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<pre style="margin: 0;">-<span id="LC469" class="line" lang="cpp"> <span class="n" style="color: #333;">zfp_</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gzopen</span><span class="p">(</span><span class="n" style="color: #333;">infiles_</span><span class="p">[</span><span class="n" style="color: #333;">filecur_</span><span class="p">].</span><span class="n" style="color: #333;">c_str</span><span class="p">(),</span> <span class="s" style="color: #d14;">"rb"</span><span class="p">);</span></span>
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470
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<pre style="margin: 0;">-<span id="LC470" class="line" lang="cpp"> <span class="p">}</span></span>
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471
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<pre style="margin: 0;">-<span id="LC471" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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472
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<pre style="margin: 0;">-<span id="LC472" class="line" lang="cpp"> <span class="n" style="color: #333;">fp_</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fopen</span><span class="p">(</span><span class="n" style="color: #333;">infiles_</span><span class="p">[</span><span class="n" style="color: #333;">filecur_</span><span class="p">].</span><span class="n" style="color: #333;">c_str</span><span class="p">(),</span> <span class="s" style="color: #d14;">"rb"</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC473" 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;">filename</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">infiles_</span><span class="p">[</span><span class="n" style="color: #333;">filecur_</span><span class="p">].</span><span class="n" style="color: #333;">c_str</span><span class="p">();</span></span>
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<pre style="margin: 0;">+<span id="LC474" class="line" lang="cpp"> <span class="n" style="color: #333;">compressed_</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">is_gzipped_file</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC475" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">compressed_</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC476" class="line" lang="cpp"> <span class="n" style="color: #333;">zfp_</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gzopen</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="p">,</span> <span class="s" style="color: #d14;">"rb"</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC477" 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="LC478" class="line" lang="cpp"> <span class="n" style="color: #333;">fp_</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fopen</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="p">,</span> <span class="s" style="color: #d14;">"rb"</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC479" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC480" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">((</span><span class="n" style="color: #333;">compressed_</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">zfp_</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">NULL</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;">compressed_</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">fp_</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">))</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC481" 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;">errs_</span><span class="p">[</span><span class="n" style="color: #333;">filecur_</span><span class="p">])</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC482" 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: Could not open read file </span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">-<span id="LC477" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;"><span class="idiff left">infiles_</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">filecur_</span></span><span class="p"><span class="idiff">].</span></span><span class="n" style="color: #333;"><span class="idiff">c_str</span></span><span class="p"><span class="idiff right">()</span></span></span>
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<pre style="margin: 0;">+<span id="LC483" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;"><span class="idiff left right">filename</span></span></span>
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<pre style="margin: 0;"> <span id="LC484" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;"> for reading; skipping..."</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="LC485" class="line" lang="cpp"> <span class="n" style="color: #333;">errs_</span><span class="p">[</span><span class="n" style="color: #333;">filecur_</span><span class="p">]</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="LC480" class="line" lang="cpp"><span class="idiff left right"> </span> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC481" class="line" lang="cpp"><span class="idiff left right"> </span> <span class="n" style="color: #333;">filecur_</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC482" class="line" lang="cpp"><span class="idiff left right"> </span> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC486" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC487" class="line" lang="cpp"> <span class="n" style="color: #333;">filecur_</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC488" 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="LC489" class="line" lang="cpp"> <span class="p">}</span></span>
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484
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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>
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485
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491
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<pre style="margin: 0;"> <span id="LC491" class="line" lang="cpp"> <span class="n" style="color: #333;">is_open_</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="1125" style="width: 35px; color: rgba(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="1131" style="width: 35px; color: rgba(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">@@ -1125,6 +1131,167 @@ bool FastqPatternSource::parse(Read &r, Read& rb, TReadId rdid) const {</td>
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1125
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1131
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<pre style="margin: 0;"> <span id="LC1131" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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1126
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1132
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<pre style="margin: 0;"> <span id="LC1132" class="line" lang="cpp"><span class="p">}</span></span>
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1127
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<td class="diff-line-num new_line" data-linenumber="1133" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1133
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<pre style="margin: 0;"> <span id="LC1133" class="line" lang="cpp"></span>
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<td class="diff-line-num new new_line" 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;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">BAMPatternSource</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">offset</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" 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="mi" style="color: #099;">0</span><span class="p">,</span> <span class="c1" style="color: #998; font-style: italic;">//refID</span></span>
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<td class="diff-line-num new new_line" 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="mi" style="color: #099;">4</span><span class="p">,</span> <span class="c1" style="color: #998; font-style: italic;">//pos</span></span>
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1137
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<pre style="margin: 0;">+<span id="LC1137" class="line" lang="cpp"> <span class="mi" style="color: #099;">8</span><span class="p">,</span> <span class="c1" style="color: #998; font-style: italic;">//l_read_name</span></span>
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<td class="diff-line-num new new_line" 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="mi" style="color: #099;">9</span><span class="p">,</span> <span class="c1" style="color: #998; font-style: italic;">//mapq</span></span>
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1139
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<pre style="margin: 0;">+<span id="LC1139" class="line" lang="cpp"> <span class="mi" style="color: #099;">10</span><span class="p">,</span> <span class="c1" style="color: #998; font-style: italic;">//bin</span></span>
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1140
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<pre style="margin: 0;">+<span id="LC1140" class="line" lang="cpp"> <span class="mi" style="color: #099;">12</span><span class="p">,</span> <span class="c1" style="color: #998; font-style: italic;">//n_cigar_op</span></span>
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1141
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<pre style="margin: 0;">+<span id="LC1141" class="line" lang="cpp"> <span class="mi" style="color: #099;">14</span><span class="p">,</span> <span class="c1" style="color: #998; font-style: italic;">//flag</span></span>
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1142
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<pre style="margin: 0;">+<span id="LC1142" class="line" lang="cpp"> <span class="mi" style="color: #099;">16</span><span class="p">,</span> <span class="c1" style="color: #998; font-style: italic;">//l_seq</span></span>
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1143
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<pre style="margin: 0;">+<span id="LC1143" class="line" lang="cpp"> <span class="mi" style="color: #099;">20</span><span class="p">,</span> <span class="c1" style="color: #998; font-style: italic;">//next_refID</span></span>
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1144
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<pre style="margin: 0;">+<span id="LC1144" class="line" lang="cpp"> <span class="mi" style="color: #099;">24</span><span class="p">,</span> <span class="c1" style="color: #998; font-style: italic;">//next_pos</span></span>
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1145
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<pre style="margin: 0;">+<span id="LC1145" class="line" lang="cpp"> <span class="mi" style="color: #099;">28</span><span class="p">,</span> <span class="c1" style="color: #998; font-style: italic;">//tlen</span></span>
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1146
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<pre style="margin: 0;">+<span id="LC1146" class="line" lang="cpp"> <span class="mi" style="color: #099;">32</span><span class="p">,</span> <span class="c1" style="color: #998; font-style: italic;">//read_name</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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1148
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<pre style="margin: 0;">+<span id="LC1148" class="line" lang="cpp"></span>
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1149
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<pre style="margin: 0;">+<span id="LC1149" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">BAMPatternSource</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">parse_bam_header</span><span class="p">()</span> <span class="p">{</span></span>
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1150
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<pre style="margin: 0;">+<span id="LC1150" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">magic</span><span class="p">[</span><span class="mi" style="color: #099;">4</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>
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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;">zread</span><span class="p">(</span><span class="n" style="color: #333;">magic</span><span class="p">,</span> <span class="mi" style="color: #099;">4</span><span class="p">)</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;">strncmp</span><span class="p">(</span><span class="n" style="color: #333;">magic</span><span class="p">,</span> <span class="s" style="color: #d14;">"BAM</span><span class="se" style="color: #d14;">\001</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 class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1153" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1153
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<pre style="margin: 0;">+<span id="LC1153" 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;">"This file is not a BAM 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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<td class="diff-line-num new new_line" data-linenumber="1154" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1154
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<pre style="margin: 0;">+<span id="LC1154" 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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<td class="diff-line-num new new_line" data-linenumber="1155" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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="diff-line-num new new_line" 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>
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<td class="diff-line-num new new_line" data-linenumber="1157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1157
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<pre style="margin: 0;">+<span id="LC1157" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">l_text</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="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="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">n_ref</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1159
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<pre style="margin: 0;">+<span id="LC1159" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">data</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1160
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<pre style="margin: 0;">+<span id="LC1160" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">size</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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1161
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<pre style="margin: 0;">+<span id="LC1161" class="line" lang="cpp"></span>
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<td class="diff-line-num new new_line" data-linenumber="1162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1162
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<pre style="margin: 0;">+<span id="LC1162" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">zread</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">l_text</span><span class="p">,</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">l_text</span><span class="p">))</span> <span class="o" style="font-weight: 600;">!=</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">l_text</span><span class="p">))</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1163" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1163
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<pre style="margin: 0;">+<span id="LC1163" 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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<td class="diff-line-num new new_line" 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="p">}</span></span>
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1165
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<pre style="margin: 0;">+<span id="LC1165" class="line" lang="cpp"></span>
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<td class="diff-line-num new new_line" 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;">size</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">l_text</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" 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;">data</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;">size</span><span class="p">];</span></span>
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<td class="diff-line-num new new_line" 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;">data</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" 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="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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1170
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<pre style="margin: 0;">+<span id="LC1170" class="line" lang="cpp"> <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="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">zread</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">,</span> <span class="n" style="color: #333;">l_text</span><span class="p">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">l_text</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1172" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1172
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<pre style="margin: 0;">+<span id="LC1172" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">delete</span><span class="p">[]</span> <span class="n" style="color: #333;">data</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1173" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1173
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<pre style="margin: 0;">+<span id="LC1173" 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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<td class="diff-line-num new new_line" data-linenumber="1174" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1174
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<pre style="margin: 0;">+<span id="LC1174" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1175" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1175
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<pre style="margin: 0;">+<span id="LC1175" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">zread</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">n_ref</span><span class="p">,</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">n_ref</span><span class="p">))</span> <span class="o" style="font-weight: 600;">!=</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">n_ref</span><span class="p">))</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1176" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1176
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<pre style="margin: 0;">+<span id="LC1176" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">delete</span><span class="p">[]</span> <span class="n" style="color: #333;">data</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1177" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1177
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<pre style="margin: 0;">+<span id="LC1177" 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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1178
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<pre style="margin: 0;">+<span id="LC1178" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1179" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1179
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<pre style="margin: 0;">+<span id="LC1179" class="line" lang="cpp"></span>
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<td class="diff-line-num new new_line" data-linenumber="1180" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1180
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<pre style="margin: 0;">+<span id="LC1180" 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_ref</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1181" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1181
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<pre style="margin: 0;">+<span id="LC1181" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">l_name</span><span class="p">,</span> <span class="n" style="color: #333;">l_ref</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1182" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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;">zread</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">l_name</span><span class="p">,</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">l_name</span><span class="p">))</span> <span class="o" style="font-weight: 600;">!=</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">l_name</span><span class="p">))</span> <span class="p">{</span></span>
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1183
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<pre style="margin: 0;">+<span id="LC1183" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">delete</span><span class="p">[]</span> <span class="n" style="color: #333;">data</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1184" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1184
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<pre style="margin: 0;">+<span id="LC1184" 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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1185
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<pre style="margin: 0;">+<span id="LC1185" class="line" lang="cpp"> <span class="p">}</span></span>
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1186
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<pre style="margin: 0;">+<span id="LC1186" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">l_name</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">size</span><span class="p">)</span> <span class="p">{</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;">size</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">l_name</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1188" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1188
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<pre style="margin: 0;">+<span id="LC1188" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">delete</span><span class="p">[]</span> <span class="n" style="color: #333;">data</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1189" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1189
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<pre style="margin: 0;">+<span id="LC1189" class="line" lang="cpp"> <span class="n" style="color: #333;">data</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;">size</span><span class="p">];</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1190" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1190
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<pre style="margin: 0;">+<span id="LC1190" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1191" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1191
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<pre style="margin: 0;">+<span id="LC1191" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">zread</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">,</span> <span class="n" style="color: #333;">l_name</span><span class="p">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">l_name</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1192" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1192
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<pre style="margin: 0;">+<span id="LC1192" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">delete</span><span class="p">[]</span> <span class="n" style="color: #333;">data</span><span class="p">;</span></span>
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1193
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<pre style="margin: 0;">+<span id="LC1193" 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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1194
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<pre style="margin: 0;">+<span id="LC1194" class="line" lang="cpp"> <span class="p">}</span></span>
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1195
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<pre style="margin: 0;">+<span id="LC1195" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">zread</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">l_ref</span><span class="p">,</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">l_ref</span><span class="p">))</span> <span class="o" style="font-weight: 600;">!=</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">l_ref</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="k" style="font-weight: 600;">delete</span><span class="p">[]</span> <span class="n" style="color: #333;">data</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="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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1198
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<pre style="margin: 0;">+<span id="LC1198" class="line" lang="cpp"> <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>
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1200
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<pre style="margin: 0;">+<span id="LC1200" class="line" lang="cpp"></span>
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1201
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<pre style="margin: 0;">+<span id="LC1201" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">delete</span><span class="p">[]</span> <span class="n" style="color: #333;">data</span><span class="p">;</span></span>
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1202
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<pre style="margin: 0;">+<span id="LC1202" class="line" lang="cpp"></span>
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1203
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<pre style="margin: 0;">+<span id="LC1203" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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1204
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<pre style="margin: 0;">+<span id="LC1204" class="line" lang="cpp"><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>
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<td class="diff-line-num new new_line" data-linenumber="1206" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1206
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<pre style="margin: 0;">+<span id="LC1206" 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;">int</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">BAMPatternSource</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">nextBatchFromFile</span><span class="p">(</span><span class="n" style="color: #333;">PerThreadReadBuf</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">pt</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1207" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1207
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<pre style="margin: 0;">+<span id="LC1207" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">batch_a</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">readi</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1208" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1208
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<pre style="margin: 0;">+<span id="LC1208" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">first_</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1209" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1209
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<pre style="margin: 0;">+<span id="LC1209" class="line" lang="cpp"> <span class="n" style="color: #333;">first_</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1210" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1210
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<pre style="margin: 0;">+<span id="LC1210" 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;">parse_bam_header</span><span class="p">())</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1211" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1211
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<pre style="margin: 0;">+<span id="LC1211" 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;">"Unable to parse BAM 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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<td class="diff-line-num new new_line" data-linenumber="1212" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1212
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<pre style="margin: 0;">+<span id="LC1212" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">make_pair</span><span class="p">(</span><span class="nb" style="color: #0086b3;">true</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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1213
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<pre style="margin: 0;">+<span id="LC1213" class="line" lang="cpp"> <span class="p">}</span></span>
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1214
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<pre style="margin: 0;">+<span id="LC1214" class="line" lang="cpp"> <span class="p">}</span></span>
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1215
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<pre style="margin: 0;">+<span id="LC1215" class="line" lang="cpp"></span>
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<td class="diff-line-num new new_line" data-linenumber="1216" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1216
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<pre style="margin: 0;">+<span id="LC1216" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">done</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1217" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1217
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<pre style="margin: 0;">+<span id="LC1217" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">read1</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 new new_line" data-linenumber="1218" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1218
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<pre style="margin: 0;">+<span id="LC1218" class="line" lang="cpp"></span>
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<td class="diff-line-num new new_line" data-linenumber="1219" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1219
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<pre style="margin: 0;">+<span id="LC1219" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">readi</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">pt</span><span class="p">.</span><span class="n" style="color: #333;">max_buf_</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1220" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1220
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<pre style="margin: 0;">+<span id="LC1220" 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="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1221" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1221
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<pre style="margin: 0;">+<span id="LC1221" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint16_t</span> <span class="n" style="color: #333;">flag</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1222" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1222
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<pre style="margin: 0;">+<span id="LC1222" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">block_size</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1223" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1223
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<pre style="margin: 0;">+<span id="LC1223" class="line" lang="cpp"> <span class="n" style="color: #333;">EList</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Read</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">readbuf</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pp_</span><span class="p">.</span><span class="n" style="color: #333;">align_paired_reads</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">read1</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">pt</span><span class="p">.</span><span class="n" style="color: #333;">bufb_</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">pt</span><span class="p">.</span><span class="n" style="color: #333;">bufa_</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1224" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1224
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<pre style="margin: 0;">+<span id="LC1224" class="line" lang="cpp"></span>
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<td class="diff-line-num new new_line" data-linenumber="1225" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1225
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<pre style="margin: 0;">+<span id="LC1225" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">r</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">zread</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">block_size</span><span class="p">,</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">block_size</span><span class="p">)))</span> <span class="o" style="font-weight: 600;">!=</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">block_size</span><span class="p">))</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1226" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1226
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<pre style="margin: 0;">+<span id="LC1226" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">make_pair</span><span class="p">(</span><span class="nb" style="color: #0086b3;">true</span><span class="p">,</span> <span class="n" style="color: #333;">readi</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1227" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1227
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<pre style="margin: 0;">+<span id="LC1227" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1228" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1228
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<pre style="margin: 0;">+<span id="LC1228" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">readbuf</span><span class="p">[</span><span class="n" style="color: #333;">readi</span><span class="p">].</span><span class="n" style="color: #333;">readOrigBuf</span><span class="p">.</span><span class="n" style="color: #333;">length</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">block_size</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1229" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1229
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<pre style="margin: 0;">+<span id="LC1229" class="line" lang="cpp"> <span class="n" style="color: #333;">readbuf</span><span class="p">[</span><span class="n" style="color: #333;">readi</span><span class="p">].</span><span class="n" style="color: #333;">readOrigBuf</span><span class="p">.</span><span class="n" style="color: #333;">resize</span><span class="p">(</span><span class="n" style="color: #333;">block_size</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1230" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1230
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<pre style="margin: 0;">+<span id="LC1230" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1231" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1231
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<pre style="margin: 0;">+<span id="LC1231" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">zread</span><span class="p">(</span><span class="n" style="color: #333;">readbuf</span><span class="p">[</span><span class="n" style="color: #333;">readi</span><span class="p">].</span><span class="n" style="color: #333;">readOrigBuf</span><span class="p">.</span><span class="n" style="color: #333;">wbuf</span><span class="p">(),</span> <span class="n" style="color: #333;">block_size</span><span class="p">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">block_size</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1232" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1232
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<pre style="margin: 0;">+<span id="LC1232" class="line" lang="cpp"> <span class="n" style="color: #333;">done</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 new new_line" data-linenumber="1233" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1233
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<pre style="margin: 0;">+<span id="LC1233" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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1234
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<pre style="margin: 0;">+<span id="LC1234" class="line" lang="cpp"> <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;">memcpy</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">flag</span><span class="p">,</span> <span class="n" style="color: #333;">readbuf</span><span class="p">[</span><span class="n" style="color: #333;">readi</span><span class="p">].</span><span class="n" style="color: #333;">readOrigBuf</span><span class="p">.</span><span class="n" style="color: #333;">buf</span><span class="p">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">offset</span><span class="p">[</span><span class="n" style="color: #333;">BAMField</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">flag</span><span class="p">],</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">flag</span><span class="p">));</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1236" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1236
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<pre style="margin: 0;">+<span id="LC1236" 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;">pp_</span><span class="p">.</span><span class="n" style="color: #333;">align_paired_reads</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">((</span><span class="n" style="color: #333;">flag</span> <span class="o" style="font-weight: 600;">&</span> <span class="mh" style="color: #099;">0x40</span><span class="p">)</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="p">(</span><span class="n" style="color: #333;">flag</span> <span class="o" style="font-weight: 600;">&</span> <span class="mh" style="color: #099;">0x80</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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1237
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<pre style="margin: 0;">+<span id="LC1237" class="line" lang="cpp"> <span class="n" style="color: #333;">readbuf</span><span class="p">[</span><span class="n" style="color: #333;">readi</span><span class="p">].</span><span class="n" style="color: #333;">readOrigBuf</span><span class="p">.</span><span class="n" style="color: #333;">clear</span><span class="p">();</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1238" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1238
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<pre style="margin: 0;">+<span id="LC1238" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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1239
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<pre style="margin: 0;">+<span id="LC1239" class="line" lang="cpp"> <span class="p">}</span></span>
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1240
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<pre style="margin: 0;">+<span id="LC1240" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">pp_</span><span class="p">.</span><span class="n" style="color: #333;">align_paired_reads</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">((</span><span class="n" style="color: #333;">flag</span> <span class="o" style="font-weight: 600;">&</span> <span class="mh" style="color: #099;">0x40</span><span class="p">)</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="p">(</span><span class="n" style="color: #333;">flag</span> <span class="o" style="font-weight: 600;">&</span> <span class="mh" style="color: #099;">0x80</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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1241
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<pre style="margin: 0;">+<span id="LC1241" class="line" lang="cpp"> <span class="n" style="color: #333;">readbuf</span><span class="p">[</span><span class="n" style="color: #333;">readi</span><span class="p">].</span><span class="n" style="color: #333;">readOrigBuf</span><span class="p">.</span><span class="n" style="color: #333;">clear</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="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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1243
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<pre style="margin: 0;">+<span id="LC1243" class="line" lang="cpp"> <span class="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="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">pp_</span><span class="p">.</span><span class="n" style="color: #333;">align_paired_reads</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">read1</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">flag</span> <span class="o" style="font-weight: 600;">&</span> <span class="mh" style="color: #099;">0x40</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="diff-line-num new new_line" data-linenumber="1245" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1245
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<pre style="margin: 0;">+<span id="LC1245" 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;">"Paired reads are out of order"</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="diff-line-num new new_line" data-linenumber="1246" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1246
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<pre style="margin: 0;">+<span id="LC1246" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">make_pair</span><span class="p">(</span><span class="nb" style="color: #0086b3;">true</span><span class="p">,</span> <span class="n" style="color: #333;">readi</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;">readi</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">readi</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1247" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1247
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<pre style="margin: 0;">+<span id="LC1247" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1248" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1248
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<pre style="margin: 0;">+<span id="LC1248" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">pp_</span><span class="p">.</span><span class="n" style="color: #333;">align_paired_reads</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">read1</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">flag</span> <span class="o" style="font-weight: 600;">&</span> <span class="mh" style="color: #099;">0x80</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="diff-line-num new new_line" data-linenumber="1249" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1249
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<pre style="margin: 0;">+<span id="LC1249" 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;">"Paired reads are out of order"</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="diff-line-num new new_line" data-linenumber="1250" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1250
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<pre style="margin: 0;">+<span id="LC1250" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">make_pair</span><span class="p">(</span><span class="nb" style="color: #0086b3;">true</span><span class="p">,</span> <span class="n" style="color: #333;">readi</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;">readi</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">readi</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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1251
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<pre style="margin: 0;">+<span id="LC1251" class="line" lang="cpp"> <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>
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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;">read1</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">read1</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;">readi</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">pp_</span><span class="p">.</span><span class="n" style="color: #333;">align_paired_reads</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1255" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1255
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<pre style="margin: 0;">+<span id="LC1255" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">pt</span><span class="p">.</span><span class="n" style="color: #333;">bufb_</span><span class="p">[</span><span class="n" style="color: #333;">readi</span><span class="p">].</span><span class="n" style="color: #333;">readOrigBuf</span><span class="p">.</span><span class="n" style="color: #333;">length</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="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">readi</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">readi</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1256" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1256
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<pre style="margin: 0;">+<span id="LC1256" class="line" lang="cpp"> <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="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">make_pair</span><span class="p">(</span><span class="n" style="color: #333;">done</span><span class="p">,</span> <span class="n" style="color: #333;">readi</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="p">}</span></span>
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1259
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<pre style="margin: 0;">+<span id="LC1259" class="line" lang="cpp"></span>
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1260
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<pre style="margin: 0;">+<span id="LC1260" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">BAMPatternSource</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">parse</span><span class="p">(</span><span class="n" style="color: #333;">Read</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">ra</span><span class="p">,</span> <span class="n" style="color: #333;">Read</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">rb</span><span class="p">,</span> <span class="n" style="color: #333;">TReadId</span> <span class="n" style="color: #333;">rdid</span><span class="p">)</span> <span class="k" style="font-weight: 600;">const</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1261" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1261
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<pre style="margin: 0;">+<span id="LC1261" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint8_t</span> <span class="n" style="color: #333;">l_read_name</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="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">l_seq</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1263" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1263
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<pre style="margin: 0;">+<span id="LC1263" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint16_t</span> <span class="n" style="color: #333;">n_cigar_op</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1264" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1264
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<pre style="margin: 0;">+<span id="LC1264" 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;">buf</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ra</span><span class="p">.</span><span class="n" style="color: #333;">readOrigBuf</span><span class="p">.</span><span class="n" style="color: #333;">buf</span><span class="p">();</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1265" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1265
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<pre style="margin: 0;">+<span id="LC1265" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">block_size</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ra</span><span class="p">.</span><span class="n" style="color: #333;">readOrigBuf</span><span class="p">.</span><span class="n" style="color: #333;">length</span><span class="p">();</span></span>
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1266
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<pre style="margin: 0;">+<span id="LC1266" class="line" lang="cpp"></span>
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<td class="diff-line-num new new_line" data-linenumber="1267" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1267
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<pre style="margin: 0;">+<span id="LC1267" 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;">l_read_name</span><span class="p">,</span> <span class="n" style="color: #333;">buf</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">offset</span><span class="p">[</span><span class="n" style="color: #333;">BAMField</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">l_read_name</span><span class="p">],</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">l_read_name</span><span class="p">));</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1268" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1268
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<pre style="margin: 0;">+<span id="LC1268" 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;">n_cigar_op</span><span class="p">,</span> <span class="n" style="color: #333;">buf</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">offset</span><span class="p">[</span><span class="n" style="color: #333;">BAMField</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">n_cigar_op</span><span class="p">],</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">n_cigar_op</span><span class="p">));</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1269" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1269
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<pre style="margin: 0;">+<span id="LC1269" 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;">l_seq</span><span class="p">,</span> <span class="n" style="color: #333;">buf</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">offset</span><span class="p">[</span><span class="n" style="color: #333;">BAMField</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">l_seq</span><span class="p">],</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">l_seq</span><span class="p">));</span></span>
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1270
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<pre style="margin: 0;">+<span id="LC1270" class="line" lang="cpp"></span>
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<td class="diff-line-num new new_line" data-linenumber="1271" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1271
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<pre style="margin: 0;">+<span id="LC1271" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">off</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">offset</span><span class="p">[</span><span class="n" style="color: #333;">BAMField</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">read_name</span><span class="p">];</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1272" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1272
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<pre style="margin: 0;">+<span id="LC1272" class="line" lang="cpp"> <span class="n" style="color: #333;">ra</span><span class="p">.</span><span class="n" style="color: #333;">name</span><span class="p">.</span><span class="n" style="color: #333;">install</span><span class="p">(</span><span class="n" style="color: #333;">buf</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">off</span><span class="p">,</span> <span class="n" style="color: #333;">l_read_name</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1273" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1273
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<pre style="margin: 0;">+<span id="LC1273" class="line" lang="cpp"> <span class="n" style="color: #333;">off</span> <span class="o" style="font-weight: 600;">+=</span> <span class="p">(</span><span class="n" style="color: #333;">l_read_name</span> <span class="o" style="font-weight: 600;">+</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">n_cigar_op</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1274" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1274
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<pre style="margin: 0;">+<span id="LC1274" 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="n" style="color: #333;">buf</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">off</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1275" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1275
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<pre style="margin: 0;">+<span id="LC1275" class="line" lang="cpp"> <span class="n" style="color: #333;">off</span> <span class="o" style="font-weight: 600;">+=</span> <span class="p">(</span><span class="n" style="color: #333;">l_seq</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">)</span><span class="o" style="font-weight: 600;">/</span><span class="mi" style="color: #099;">2</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1276" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1276
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<pre style="margin: 0;">+<span id="LC1276" 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;">qual</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">buf</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">off</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1277" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1277
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<pre style="margin: 0;">+<span id="LC1277" 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;">l_seq</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1278" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1278
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<pre style="margin: 0;">+<span id="LC1278" class="line" lang="cpp"> <span class="n" style="color: #333;">ra</span><span class="p">.</span><span class="n" style="color: #333;">qual</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">qual</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">33</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1279" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1279
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<pre style="margin: 0;">+<span id="LC1279" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">base</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"=ACMGRSVTWYHKDBN"</span><span class="p">[</span><span class="k" style="font-weight: 600;">static_cast</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">uint8_t</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="n" style="color: #333;">seq</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;">2</span><span class="p">])</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="p">(</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">-</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;">2</span><span class="p">))</span> <span class="o" style="font-weight: 600;">&</span> <span class="mh" style="color: #099;">0xf</span><span class="p">];</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1280" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1280
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<pre style="margin: 0;">+<span id="LC1280" class="line" lang="cpp"> <span class="n" style="color: #333;">ra</span><span class="p">.</span><span class="n" style="color: #333;">patFw</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">asc2dna</span><span class="p">[</span><span class="n" style="color: #333;">base</span><span class="p">]);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1281" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1281
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<pre style="margin: 0;">+<span id="LC1281" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1282" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1282
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<pre style="margin: 0;">+<span id="LC1282" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">pp_</span><span class="p">.</span><span class="n" style="color: #333;">preserve_sam_tags</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1283" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1283
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<pre style="margin: 0;">+<span id="LC1283" class="line" lang="cpp"> <span class="n" style="color: #333;">off</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">l_seq</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1284" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1284
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<pre style="margin: 0;">+<span id="LC1284" class="line" lang="cpp"> <span class="n" style="color: #333;">ra</span><span class="p">.</span><span class="n" style="color: #333;">preservedOptFlags</span><span class="p">.</span><span class="n" style="color: #333;">install</span><span class="p">(</span><span class="n" style="color: #333;">buf</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">off</span><span class="p">,</span> <span class="n" style="color: #333;">block_size</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">off</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1285" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1285
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<pre style="margin: 0;">+<span id="LC1285" class="line" lang="cpp"> <span class="p">}</span></span>
</pre>
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1286
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<pre style="margin: 0;">+<span id="LC1286" class="line" lang="cpp"></span>
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<td class="diff-line-num new new_line" data-linenumber="1287" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1287
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<pre style="margin: 0;">+<span id="LC1287" class="line" lang="cpp"> <span class="n" style="color: #333;">ra</span><span class="p">.</span><span class="n" style="color: #333;">parsed</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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1288
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<pre style="margin: 0;">+<span id="LC1288" 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;">rb</span><span class="p">.</span><span class="n" style="color: #333;">parsed</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">rb</span><span class="p">.</span><span class="n" style="color: #333;">readOrigBuf</span><span class="p">.</span><span class="n" style="color: #333;">length</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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1289
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<pre style="margin: 0;">+<span id="LC1289" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">parse</span><span class="p">(</span><span class="n" style="color: #333;">rb</span><span class="p">,</span> <span class="n" style="color: #333;">ra</span><span class="p">,</span> <span class="n" style="color: #333;">rdid</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC1290" class="line" lang="cpp"> <span class="p">}</span></span>
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1291
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<pre style="margin: 0;">+<span id="LC1291" class="line" lang="cpp"></span>
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1292
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<pre style="margin: 0;">+<span id="LC1292" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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1293
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<pre style="margin: 0;">+<span id="LC1293" class="line" lang="cpp"><span class="p">}</span></span>
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1294
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<pre style="margin: 0;">+<span id="LC1294" class="line" lang="cpp"></span>
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1295
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<pre style="margin: 0;"> <span id="LC1295" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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1129
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1296
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<pre style="margin: 0;"> <span id="LC1296" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Light-parse a batch of tabbed-format reads into given buffer.</span></span>
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1297
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<pre style="margin: 0;"> <span id="LC1297" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<a href="https://salsa.debian.org/med-team/bowtie2/commit/157dbc209f47672a9a7167d16e3a324803906000#6c8922e214bc665a49b5acea11b505cbd36446c5"><strong>pat.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">@@ -62,11 +62,14 @@ struct PatternParams {</td>
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">intQuals_</span><span class="p">,</span></span>
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63
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63
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">trim5_</span><span class="p">,</span></span>
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64
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64
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">trim3_</span><span class="p">,</span></span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="c"> <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;">short</span><span class="p">,</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;">trimTo_</span><span class="p">,</span></span>
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66
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">sampleLen_</span><span class="p">,</span></span>
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67
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">sampleFreq_</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="c"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">skip_</span><span class="p">,</span></span>
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69
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nthreads_</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">fixName_</span><span class="p">)</span> <span class="o" style="font-weight: 600;">:</span></span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">fixName_</span><span class="p">,</span></span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">preserve_sam_tags_</span><span class="p">,</span></span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">align_paired_reads_</span><span class="p">)</span> <span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="c"> <span class="n" style="color: #333;">format</span><span class="p">(</span><span class="n" style="color: #333;">format_</span><span class="p">),</span></span>
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="c"> <span class="n" style="color: #333;">fileParallel</span><span class="p">(</span><span class="n" style="color: #333;">fileParallel_</span><span class="p">),</span></span>
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="c"> <span class="n" style="color: #333;">seed</span><span class="p">(</span><span class="n" style="color: #333;">seed_</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">@@ -76,11 +79,14 @@ struct PatternParams {</td>
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="c"> <span class="n" style="color: #333;">intQuals</span><span class="p">(</span><span class="n" style="color: #333;">intQuals_</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;">trim5</span><span class="p">(</span><span class="n" style="color: #333;">trim5_</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;">trim3</span><span class="p">(</span><span class="n" style="color: #333;">trim3_</span><span class="p">),</span></span>
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="c"> <span class="n" style="color: #333;">trimTo</span><span class="p">(</span><span class="n" style="color: #333;">trimTo_</span><span class="p">),</span></span>
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="c"> <span class="n" style="color: #333;">sampleLen</span><span class="p">(</span><span class="n" style="color: #333;">sampleLen_</span><span class="p">),</span></span>
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="c"> <span class="n" style="color: #333;">sampleFreq</span><span class="p">(</span><span class="n" style="color: #333;">sampleFreq_</span><span class="p">),</span></span>
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="c"> <span class="n" style="color: #333;">skip</span><span class="p">(</span><span class="n" style="color: #333;">skip_</span><span class="p">),</span></span>
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="c"> <span class="n" style="color: #333;">nthreads</span><span class="p">(</span><span class="n" style="color: #333;">nthreads_</span><span class="p">),</span></span>
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<pre style="margin: 0;">-<span id="LC83" class="line" lang="c"> <span class="n" style="color: #333;">fixName</span><span class="p">(</span><span class="n" style="color: #333;">fixName_</span><span class="p">)</span> <span class="p">{</span> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="c"> <span class="n" style="color: #333;">fixName</span><span class="p">(</span><span class="n" style="color: #333;">fixName_</span><span class="p">),</span></span>
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="c"> <span class="n" style="color: #333;">preserve_sam_tags</span><span class="p">(</span><span class="n" style="color: #333;">preserve_sam_tags_</span><span class="p">),</span></span>
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="c"> <span class="n" style="color: #333;">align_paired_reads</span><span class="p">(</span><span class="n" style="color: #333;">align_paired_reads_</span><span class="p">)</span> <span class="p">{</span> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">format</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// file format</span></span>
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">fileParallel</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// true -> wrap files with separate PatternComposers</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">@@ -91,11 +97,14 @@ struct PatternParams {</td>
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<pre style="margin: 0;"> <span id="LC97" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">intQuals</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// true -> qualities are space-separated numbers</span></span>
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98
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<pre style="margin: 0;"> <span id="LC98" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">trim5</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// amt to hard clip from 5' end</span></span>
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">trim3</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// amt to hard clip from 3' end</span></span>
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="c"> <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;">short</span><span class="p">,</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;">trimTo</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC101" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">sampleLen</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// length of sampled reads for FastaContinuous...</span></span>
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102
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<pre style="margin: 0;"> <span id="LC102" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">sampleFreq</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// frequency of sampled reads for FastaContinuous...</span></span>
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103
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">skip</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// skip the first 'skip' patterns</span></span>
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97
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104
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<pre style="margin: 0;"> <span id="LC104" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nthreads</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// number of threads for locking</span></span>
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98
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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;">bool</span> <span class="n" style="color: #333;">fixName</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">//</span></span>
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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;">preserve_sam_tags</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// keep existing SAM tags when aligning BAM files</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;">align_paired_reads</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC108" class="line" lang="c"><span class="p">};</span></span>
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109
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<pre style="margin: 0;"> <span id="LC109" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC110" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/**</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">@@ -153,7 +162,7 @@ struct PerThreadReadBuf {</td>
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<pre style="margin: 0;"> <span id="LC162" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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154
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<pre style="margin: 0;"> <span id="LC163" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">exhausted</span><span class="p">()</span> <span class="p">{</span></span>
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155
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164
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<pre style="margin: 0;"> <span id="LC164" class="line" lang="c"> <span class="n" style="color: #333;">assert_leq</span><span class="p">(</span><span class="n" style="color: #333;">cur_buf_</span><span class="p">,</span> <span class="n" style="color: #333;">bufa_</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">());</span></span>
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156
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<pre style="margin: 0;">-<span id="LC156" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">cur_buf_</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">bufa_</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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<pre style="margin: 0;">+<span id="LC165" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">cur_buf_</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">bufa_</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="n" style="color: #333;"><span class="idiff">bufa_</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">cur_buf_</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">].</span></span><span class="n" style="color: #333;"><span class="idiff">readOrigBuf</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">empty</span></span><span class="p"><span class="idiff right">()</span>;</span></span>
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<pre style="margin: 0;"> <span id="LC166" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC167" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC168" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/**</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">@@ -403,21 +412,34 @@ protected:</td>
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<pre style="margin: 0;"> <span id="LC412" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">compressed_</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">gzungetc</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">,</span> <span class="n" style="color: #333;">zfp_</span><span class="p">)</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">ungetc</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">,</span> <span class="n" style="color: #333;">fp_</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC413" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC414" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC406" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="nf" style="color: #900; font-weight: 600;">is_gzipped_file</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="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC407" class="line" lang="c"> <span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">stat</span> <span class="n" style="color: #333;">s</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC408" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">stat</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="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">s</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="LC409" class="line" lang="c"> <span class="n" style="color: #333;">perror</span><span class="p">(</span><span class="s" style="color: #d14;">"stat"</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="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">zread</span><span class="p">(</span><span class="n" style="color: #333;">voidp</span> <span class="n" style="color: #333;">buf</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</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="LC416" 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="n" style="color: #333;">gzread</span><span class="p">(</span><span class="n" style="color: #333;">zfp_</span><span class="p">,</span> <span class="n" style="color: #333;">buf</span><span class="p">,</span> <span class="n" style="color: #333;">len</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC417" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</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 class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC418" class="line" lang="c"> <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;">err</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gzerror</span><span class="p">(</span><span class="n" style="color: #333;">zfp_</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC419" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">err</span> <span class="o" style="font-weight: 600;">!=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC420" 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;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">err</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="LC421" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC422" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC411" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC412" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">S_ISFIFO</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">st_mode</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC413" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC423" 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="LC424" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC425" class="line" lang="c"></span>
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426
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<pre style="margin: 0;">+<span id="LC426" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="nf" style="color: #900; font-weight: 600;">is_gzipped_file</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;">filename</span><span class="p">)</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="c"> <span class="kt" style="color: #458; font-weight: 600;">FILE</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">f</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fopen</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="p">,</span> <span class="s" style="color: #d14;">"rb"</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="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">ferror</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;">0</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="c"> <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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414
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430
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<pre style="margin: 0;"> <span id="LC430" class="line" lang="c"> <span class="p">}</span></span>
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415
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<pre style="margin: 0;">-<span id="LC415" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">filename</span><span class="p">.</span><span class="n" style="color: #333;">find_last_of</span><span class="p">(</span><span class="s" style="color: #d14;">"."</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="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;">ext</span> <span class="o" style="font-weight: 600;">=</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;">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;">npos</span><span class="p">)</span> <span class="o" style="font-weight: 600;">?</span> <span class="s" style="color: #d14;">""</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">filename</span><span class="p">.</span><span class="n" style="color: #333;">substr</span><span class="p">(</span><span class="n" style="color: #333;">pos</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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417
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<pre style="margin: 0;">-<span id="LC417" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">ext</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">""</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">ext</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"gz"</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">ext</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"Z"</span><span class="p">)</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="c"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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431
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<pre style="margin: 0;">+<span id="LC431" class="line" lang="c"></span>
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432
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<pre style="margin: 0;">+<span id="LC432" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <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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433
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<pre style="margin: 0;">+<span id="LC433" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">uint8_t</span> <span class="n" style="color: #333;">byte1</span><span class="p">,</span> <span class="n" style="color: #333;">byte2</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="c"></span>
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435
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<pre style="margin: 0;">+<span id="LC435" class="line" lang="c"> <span class="n" style="color: #333;">fread</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">byte1</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint8_t</span><span class="p">),</span> <span class="n" style="color: #333;">f</span><span class="p">);</span></span>
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436
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<pre style="margin: 0;">+<span id="LC436" class="line" lang="c"> <span class="n" style="color: #333;">fread</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">byte2</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint8_t</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="LC437" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">byte1</span> <span class="o" style="font-weight: 600;">==</span> <span class="mh" style="color: #099;">0x1f</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">byte2</span> <span class="o" style="font-weight: 600;">==</span> <span class="mh" style="color: #099;">0x8b</span><span class="p">)</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="c"> <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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419
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<pre style="margin: 0;"> <span id="LC439" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC420" class="line" lang="c"> <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="LC440" class="line" lang="c"> <span class="n" style="color: #333;">fclose</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="LC441" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC442" class="line" lang="c"> <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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443
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<pre style="margin: 0;"> <span id="LC443" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC444" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC445" class="line" lang="c"> <span class="n" style="color: #333;">EList</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;">infiles_</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// filenames for read files</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">@@ -696,6 +718,68 @@ protected:</td>
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<pre style="margin: 0;"> <span id="LC718" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">interleaved_</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// fastq reads are interleaved</span></span>
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<pre style="margin: 0;"> <span id="LC719" class="line" lang="c"><span class="p">};</span></span>
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<pre style="margin: 0;"> <span id="LC720" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC721" class="line" lang="c"><span class="n" style="color: #333;">class</span> <span class="n" style="color: #333;">BAMPatternSource</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">public</span> <span class="n" style="color: #333;">CFilePatternSource</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC722" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC723" class="line" lang="c"><span class="n" style="color: #333;">public</span><span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;">+<span id="LC724" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC725" class="line" lang="c"> <span class="n" style="color: #333;">BAMPatternSource</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC726" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">EList</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;">infiles</span><span class="p">,</span></span>
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727
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<pre style="margin: 0;">+<span id="LC727" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">PatternParams</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">p</span><span class="p">)</span> <span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;">+<span id="LC728" class="line" lang="c"> <span class="n" style="color: #333;">CFilePatternSource</span><span class="p">(</span><span class="n" style="color: #333;">infiles</span><span class="p">,</span> <span class="n" style="color: #333;">p</span><span class="p">),</span></span>
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729
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<pre style="margin: 0;">+<span id="LC729" class="line" lang="c"> <span class="n" style="color: #333;">first_</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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730
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<pre style="margin: 0;">+<span id="LC730" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC731" class="line" lang="c"> <span class="k" style="font-weight: 600;">virtual</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">reset</span><span class="p">()</span> <span class="p">{</span></span>
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732
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<pre style="margin: 0;">+<span id="LC732" class="line" lang="c"> <span class="n" style="color: #333;">first_</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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733
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<pre style="margin: 0;">+<span id="LC733" class="line" lang="c"> <span class="n" style="color: #333;">CFilePatternSource</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">reset</span><span class="p">();</span></span>
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<pre style="margin: 0;">+<span id="LC734" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC736" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">+<span id="LC737" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * Finalize BAM parsing outside critical section.</span></span>
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<pre style="margin: 0;">+<span id="LC738" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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739
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<pre style="margin: 0;">+<span id="LC739" class="line" lang="c"> <span class="k" style="font-weight: 600;">virtual</span> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">parse</span><span class="p">(</span><span class="n" style="color: #333;">Read</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">ra</span><span class="p">,</span> <span class="n" style="color: #333;">Read</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">rb</span><span class="p">,</span> <span class="n" style="color: #333;">TReadId</span> <span class="n" style="color: #333;">rdid</span><span class="p">)</span> <span class="k" style="font-weight: 600;">const</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="c"></span>
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<pre style="margin: 0;">+<span id="LC741" class="line" lang="c"><span class="n" style="color: #333;">protected</span><span class="o" style="font-weight: 600;">:</span></span>
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742
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743
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<pre style="margin: 0;">+<span id="LC743" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">+<span id="LC744" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * Light-parse a batch into the given buffer.</span></span>
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<pre style="margin: 0;">+<span id="LC745" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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746
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<pre style="margin: 0;">+<span id="LC746" class="line" lang="c"> <span class="k" style="font-weight: 600;">virtual</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">pair</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">bool</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">nextBatchFromFile</span><span class="p">(</span><span class="n" style="color: #333;">PerThreadReadBuf</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">pt</span><span class="p">,</span> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">batch_a</span><span class="p">,</span></span>
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747
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<pre style="margin: 0;">+<span id="LC747" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">readi</span><span class="p">);</span></span>
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748
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<pre style="margin: 0;">+<span id="LC748" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC750" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">+<span id="LC751" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * Reset state to be ready for the next file.</span></span>
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<pre style="margin: 0;">+<span id="LC752" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">+<span id="LC753" class="line" lang="c"> <span class="k" style="font-weight: 600;">virtual</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">resetForNextFile</span><span class="p">()</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC754" class="line" lang="c"> <span class="n" style="color: #333;">first_</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="LC755" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC757" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">first_</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// parsing first read in file</span></span>
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758
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<pre style="margin: 0;">+<span id="LC758" class="line" lang="c"></span>
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759
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<pre style="margin: 0;">+<span id="LC759" class="line" lang="c"><span class="n" style="color: #333;">private</span><span class="o" style="font-weight: 600;">:</span></span>
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760
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<pre style="margin: 0;">+<span id="LC760" class="line" lang="c"></span>
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761
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<pre style="margin: 0;">+<span id="LC761" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">parse_bam_header</span><span class="p">();</span></span>
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762
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<pre style="margin: 0;">+<span id="LC762" class="line" lang="c"></span>
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763
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<pre style="margin: 0;">+<span id="LC763" class="line" lang="c"> <span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">BAMField</span> <span class="p">{</span></span>
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764
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<pre style="margin: 0;">+<span id="LC764" class="line" lang="c"> <span class="k" style="font-weight: 600;">enum</span> <span class="n" style="color: #333;">aln_rec_field_name</span> <span class="p">{</span></span>
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765
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<pre style="margin: 0;">+<span id="LC765" class="line" lang="c"> <span class="n" style="color: #333;">refID</span><span class="p">,</span></span>
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766
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<pre style="margin: 0;">+<span id="LC766" class="line" lang="c"> <span class="n" style="color: #333;">pos</span><span class="p">,</span></span>
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767
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<pre style="margin: 0;">+<span id="LC767" class="line" lang="c"> <span class="n" style="color: #333;">l_read_name</span><span class="p">,</span></span>
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768
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<pre style="margin: 0;">+<span id="LC768" class="line" lang="c"> <span class="n" style="color: #333;">mapq</span><span class="p">,</span></span>
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769
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<pre style="margin: 0;">+<span id="LC769" class="line" lang="c"> <span class="n" style="color: #333;">bin</span><span class="p">,</span></span>
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770
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<pre style="margin: 0;">+<span id="LC770" class="line" lang="c"> <span class="n" style="color: #333;">n_cigar_op</span><span class="p">,</span></span>
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771
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<pre style="margin: 0;">+<span id="LC771" class="line" lang="c"> <span class="n" style="color: #333;">flag</span><span class="p">,</span></span>
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772
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<pre style="margin: 0;">+<span id="LC772" class="line" lang="c"> <span class="n" style="color: #333;">l_seq</span><span class="p">,</span></span>
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773
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<pre style="margin: 0;">+<span id="LC773" class="line" lang="c"> <span class="n" style="color: #333;">next_refID</span><span class="p">,</span></span>
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774
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<pre style="margin: 0;">+<span id="LC774" class="line" lang="c"> <span class="n" style="color: #333;">next_pos</span><span class="p">,</span></span>
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775
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<pre style="margin: 0;">+<span id="LC775" class="line" lang="c"> <span class="n" style="color: #333;">tlen</span><span class="p">,</span></span>
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776
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<pre style="margin: 0;">+<span id="LC776" class="line" lang="c"> <span class="n" style="color: #333;">read_name</span><span class="p">,</span></span>
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777
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<pre style="margin: 0;">+<span id="LC777" class="line" lang="c"> <span class="p">};</span></span>
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778
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<pre style="margin: 0;">+<span id="LC778" class="line" lang="c"> <span class="p">};</span></span>
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779
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<pre style="margin: 0;">+<span id="LC779" class="line" lang="c"></span>
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780
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<pre style="margin: 0;">+<span id="LC780" class="line" lang="c"> <span class="k" style="font-weight: 600;">static</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;">offset</span><span class="p">[];</span></span>
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781
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<pre style="margin: 0;">+<span id="LC781" class="line" lang="c"><span class="p">};</span></span>
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<pre style="margin: 0;">+<span id="LC782" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC783" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;"> <span id="LC784" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * Read a Raw-format file (one sequence per line). No quality strings</span></span>
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<pre style="margin: 0;"> <span id="LC785" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * allowed. All qualities are assumed to be 'I' (40 on the Phred-33</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">@@ -988,6 +1072,27 @@ private:</td>
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1072
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<pre style="margin: 0;"> <span id="LC1072" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">composer_</span><span class="p">.</span><span class="n" style="color: #333;">parse</span><span class="p">(</span><span class="n" style="color: #333;">ra</span><span class="p">,</span> <span class="n" style="color: #333;">rb</span><span class="p">,</span> <span class="n" style="color: #333;">buf_</span><span class="p">.</span><span class="n" style="color: #333;">rdid</span><span class="p">());</span></span>
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1073
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<pre style="margin: 0;"> <span id="LC1073" class="line" lang="c"> <span class="p">}</span></span>
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990
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1074
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<pre style="margin: 0;"> <span id="LC1074" class="line" lang="c"></span>
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1075
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<pre style="margin: 0;">+<span id="LC1075" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">trim</span><span class="p">(</span><span class="n" style="color: #333;">Read</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">r</span><span class="p">)</span> <span class="p">{</span></span>
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1076
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<pre style="margin: 0;">+<span id="LC1076" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">pp_</span><span class="p">.</span><span class="n" style="color: #333;">trimTo</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="p">)</span> <span class="p">{</span></span>
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1077
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<pre style="margin: 0;">+<span id="LC1077" class="line" lang="c"> <span class="k" style="font-weight: 600;">switch</span> <span class="p">(</span><span class="n" style="color: #333;">pp_</span><span class="p">.</span><span class="n" style="color: #333;">trimTo</span><span class="p">.</span><span class="n" style="color: #333;">first</span><span class="p">)</span> <span class="p">{</span></span>
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1078
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<pre style="margin: 0;">+<span id="LC1078" class="line" lang="c"> <span class="k" style="font-weight: 600;">case</span> <span class="mi" style="color: #099;">3</span><span class="p">:</span></span>
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1079
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<pre style="margin: 0;">+<span id="LC1079" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">r</span><span class="p">.</span><span class="n" style="color: #333;">patFw</span><span class="p">.</span><span class="n" style="color: #333;">length</span><span class="p">()</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">pp_</span><span class="p">.</span><span class="n" style="color: #333;">trimTo</span><span class="p">.</span><span class="n" style="color: #333;">second</span><span class="p">)</span> <span class="p">{</span></span>
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1080
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<pre style="margin: 0;">+<span id="LC1080" class="line" lang="c"> <span class="n" style="color: #333;">r</span><span class="p">.</span><span class="n" style="color: #333;">trimmed5</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">r</span><span class="p">.</span><span class="n" style="color: #333;">patFw</span><span class="p">.</span><span class="n" style="color: #333;">length</span><span class="p">()</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">pp_</span><span class="p">.</span><span class="n" style="color: #333;">trimTo</span><span class="p">.</span><span class="n" style="color: #333;">second</span><span class="p">;</span></span>
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1081
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<pre style="margin: 0;">+<span id="LC1081" class="line" lang="c"> <span class="n" style="color: #333;">r</span><span class="p">.</span><span class="n" style="color: #333;">patFw</span><span class="p">.</span><span class="n" style="color: #333;">trimEnd</span><span class="p">(</span><span class="n" style="color: #333;">r</span><span class="p">.</span><span class="n" style="color: #333;">trimmed5</span><span class="p">);</span></span>
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1082
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<pre style="margin: 0;">+<span id="LC1082" class="line" lang="c"> <span class="n" style="color: #333;">r</span><span class="p">.</span><span class="n" style="color: #333;">qual</span><span class="p">.</span><span class="n" style="color: #333;">trimEnd</span><span class="p">(</span><span class="n" style="color: #333;">r</span><span class="p">.</span><span class="n" style="color: #333;">trimmed5</span><span class="p">);</span></span>
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1083
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<pre style="margin: 0;">+<span id="LC1083" class="line" lang="c"> <span class="p">}</span></span>
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1084
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<pre style="margin: 0;">+<span id="LC1084" class="line" lang="c"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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1085
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<pre style="margin: 0;">+<span id="LC1085" class="line" lang="c"> <span class="k" style="font-weight: 600;">case</span> <span class="mi" style="color: #099;">5</span><span class="p">:</span></span>
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1086
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<pre style="margin: 0;">+<span id="LC1086" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">r</span><span class="p">.</span><span class="n" style="color: #333;">patFw</span><span class="p">.</span><span class="n" style="color: #333;">length</span><span class="p">()</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">pp_</span><span class="p">.</span><span class="n" style="color: #333;">trimTo</span><span class="p">.</span><span class="n" style="color: #333;">second</span><span class="p">)</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="c"> <span class="n" style="color: #333;">r</span><span class="p">.</span><span class="n" style="color: #333;">trimmed3</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">r</span><span class="p">.</span><span class="n" style="color: #333;">patFw</span><span class="p">.</span><span class="n" style="color: #333;">length</span><span class="p">()</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">pp_</span><span class="p">.</span><span class="n" style="color: #333;">trimTo</span><span class="p">.</span><span class="n" style="color: #333;">second</span><span class="p">;</span></span>
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1088
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<pre style="margin: 0;">+<span id="LC1088" class="line" lang="c"> <span class="n" style="color: #333;">r</span><span class="p">.</span><span class="n" style="color: #333;">patFw</span><span class="p">.</span><span class="n" style="color: #333;">trimBegin</span><span class="p">(</span><span class="n" style="color: #333;">r</span><span class="p">.</span><span class="n" style="color: #333;">trimmed3</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC1089" class="line" lang="c"> <span class="n" style="color: #333;">r</span><span class="p">.</span><span class="n" style="color: #333;">qual</span><span class="p">.</span><span class="n" style="color: #333;">trimBegin</span><span class="p">(</span><span class="n" style="color: #333;">r</span><span class="p">.</span><span class="n" style="color: #333;">trimmed3</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC1090" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC1092" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC1093" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC1094" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC1096" class="line" lang="c"> <span class="n" style="color: #333;">PatternComposer</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">composer_</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// pattern composer</span></span>
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<pre style="margin: 0;"> <span id="LC1097" class="line" lang="c"> <span class="n" style="color: #333;">PerThreadReadBuf</span> <span class="n" style="color: #333;">buf_</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// read data buffer</span></span>
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<pre style="margin: 0;"> <span id="LC1098" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">PatternParams</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">pp_</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// pattern-related parameters</span></span>
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<a href="https://salsa.debian.org/med-team/bowtie2/commit/157dbc209f47672a9a7167d16e3a324803906000#9fc1681b02d842aa2b7bb9db116eff864b181fdf"><strong>presets.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">@@ -71,7 +71,8 @@ void PresetsV0::apply(</td>
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="cpp"> <span class="n" style="color: #333;">policy</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">";ROUNDS=1"</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="cpp"> <span class="n" style="color: #333;">policy</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">";IVAL=S,1,2.00"</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC73" 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;">preset</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"fast-local"</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC74" class="line" lang="cpp"> <span class="n" style="color: #333;">policy</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">";SEED=0,22"</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="cpp"> <span class="n" style="color: #333;">policy</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">";SEED=0"</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="cpp"> <span class="n" style="color: #333;">policy</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">";SEEDLEN=22"</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;">policy</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">";DPS=10"</span><span class="p">;</span></span>
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77
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="cpp"> <span class="n" style="color: #333;">policy</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">";ROUNDS=2"</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="cpp"> <span class="n" style="color: #333;">policy</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">";IVAL=S,1,1.75"</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">@@ -55,6 +55,7 @@ struct Read {</td>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="c"> <span class="n" style="color: #333;">patRcRev</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="LC56" class="line" lang="c"> <span class="n" style="color: #333;">qualRev</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="LC57" class="line" lang="c"> <span class="n" style="color: #333;">name</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="LC58" class="line" lang="c"> <span class="n" style="color: #333;">preservedOptFlags</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="LC59" class="line" lang="c"> <span class="n" style="color: #333;">filter</span> <span class="o" style="font-weight: 600;">=</span> <span class="sc" style="color: #d14;">'?'</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="c"> <span class="n" style="color: #333;">seed</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="LC61" class="line" lang="c"> <span class="n" style="color: #333;">parsed</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="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -254,6 +255,7 @@ struct Read {</td>
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<pre style="margin: 0;"> <span id="LC255" class="line" lang="c"> <span class="n" style="color: #333;">TBuf</span> <span class="n" style="color: #333;">readOrigBuf</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC256" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC257" class="line" lang="c"> <span class="n" style="color: #333;">BTString</span> <span class="n" style="color: #333;">name</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// read name</span></span>
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<pre style="margin: 0;">+<span id="LC258" class="line" lang="c"> <span class="n" style="color: #333;">BTString</span> <span class="n" style="color: #333;">preservedOptFlags</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC259" class="line" lang="c"> <span class="n" style="color: #333;">TReadId</span> <span class="n" style="color: #333;">rdid</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// 0-based id based on pair's offset in read file(s)</span></span>
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<pre style="margin: 0;"> <span id="LC260" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">mate</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// 0 = single-end, 1 = mate1, 2 = mate2</span></span>
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<pre style="margin: 0;"> <span id="LC261" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">seed</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// random seed</span></span>
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<a href="https://salsa.debian.org/med-team/bowtie2/commit/157dbc209f47672a9a7167d16e3a324803906000#66965a83f981ce6b0882f308dd88614650b6582c"><strong>ref_read.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">@@ -273,12 +273,16 @@ fastaRefReadSizes(</td>
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<pre style="margin: 0;"> <span id="LC273" 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;">e</span><span class="p">.</span><span class="n" style="color: #333;">what</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC274" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">throw</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC275" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC276" class="line" lang="cpp"> <span class="n" style="color: #333;">first</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="LC277" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Add the length of this record.</span></span>
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<pre style="margin: 0;">-<span id="LC277" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">rec</span><span class="p">.</span><span class="n" style="color: #333;">first</span><span class="p">)</span> <span class="n" style="color: #333;">numSeqs</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC278" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">rec</span><span class="p">.</span><span class="n" style="color: #333;">len</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;">rec</span><span class="p">.</span><span class="n" style="color: #333;">first</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC279" 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="LC280" 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;">rec</span><span class="p">.</span><span class="n" style="color: #333;">first</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC281" class="line" lang="cpp"> <span class="n" style="color: #333;">numSeqs</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC282" class="line" lang="cpp"> <span class="p">}</span></span>
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278
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283
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<pre style="margin: 0;"> <span id="LC283" class="line" lang="cpp"> <span class="n" style="color: #333;">unambigTot</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">rec</span><span class="p">.</span><span class="n" style="color: #333;">len</span><span class="p">;</span></span>
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279
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284
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<pre style="margin: 0;"> <span id="LC284" class="line" lang="cpp"> <span class="n" style="color: #333;">bothTot</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">rec</span><span class="p">.</span><span class="n" style="color: #333;">len</span><span class="p">;</span></span>
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280
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285
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<pre style="margin: 0;"> <span id="LC285" class="line" lang="cpp"> <span class="n" style="color: #333;">bothTot</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">rec</span><span class="p">.</span><span class="n" style="color: #333;">off</span><span class="p">;</span></span>
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281
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<pre style="margin: 0;">-<span id="LC281" class="line" lang="cpp"> <span class="n" style="color: #333;">first</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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282
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286
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<pre style="margin: 0;"> <span id="LC286" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">rec</span><span class="p">.</span><span class="n" style="color: #333;">len</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;">rec</span><span class="p">.</span><span class="n" style="color: #333;">off</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;">rec</span><span class="p">.</span><span class="n" style="color: #333;">first</span><span class="p">)</span> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC287" class="line" lang="cpp"> <span class="n" style="color: #333;">recs</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">rec</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC288" class="line" lang="cpp"> <span class="p">}</span></span>
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<a href="https://salsa.debian.org/med-team/bowtie2/commit/157dbc209f47672a9a7167d16e3a324803906000#8cb73317275ca3f68e13f1344310abe501fa6653"><strong>sam.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">@@ -873,3 +873,92 @@ void SamConfig::printEmptyOptFlags(</td>
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<pre style="margin: 0;"> <span id="LC873" class="line" lang="cpp"> <span class="n" style="color: #333;">printOptFieldNewlineEscapedZ</span><span class="p">(</span><span class="n" style="color: #333;">o</span><span class="p">,</span> <span class="n" style="color: #333;">rd</span><span class="p">.</span><span class="n" style="color: #333;">readOrigBuf</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC874" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC875" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC876" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC877" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">SamConfig</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">printPreservedOptFlags</span><span class="p">(</span><span class="n" style="color: #333;">BTString</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">o</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Read</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">rd</span><span class="p">)</span> <span class="k" style="font-weight: 600;">const</span> <span class="p">{</span></span>
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878
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<pre style="margin: 0;">+<span id="LC878" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">rd</span><span class="p">.</span><span class="n" style="color: #333;">preservedOptFlags</span><span class="p">.</span><span class="n" style="color: #333;">length</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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879
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<pre style="margin: 0;">+<span id="LC879" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">buf</span><span class="p">[</span><span class="mi" style="color: #099;">1024</span><span class="p">];</span></span>
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880
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<pre style="margin: 0;">+<span id="LC880" class="line" lang="cpp"> <span class="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;">b</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rd</span><span class="p">.</span><span class="n" style="color: #333;">preservedOptFlags</span><span class="p">.</span><span class="n" style="color: #333;">buf</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="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;">len</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rd</span><span class="p">.</span><span class="n" style="color: #333;">preservedOptFlags</span><span class="p">.</span><span class="n" style="color: #333;">length</span><span class="p">();</span></span>
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882
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<pre style="margin: 0;">+<span id="LC882" class="line" lang="cpp"> <span class="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;">len</span><span class="p">)</span> <span class="p">{</span></span>
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883
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<pre style="margin: 0;">+<span id="LC883" class="line" lang="cpp"> <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="sc" style="color: #d14;">'\t'</span><span class="p">);</span></span>
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884
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<pre style="margin: 0;">+<span id="LC884" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">tag</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">],</span> <span class="n" style="color: #333;">val_type</span><span class="p">;</span></span>
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885
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<pre style="margin: 0;">+<span id="LC885" class="line" lang="cpp"> <span class="n" style="color: #333;">memcpy</span><span class="p">(</span><span class="n" style="color: #333;">tag</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;">i</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">*</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="p">));</span></span>
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886
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<pre style="margin: 0;">+<span id="LC886" class="line" lang="cpp"> <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">tag</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">);</span></span>
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887
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<pre style="margin: 0;">+<span id="LC887" class="line" lang="cpp"> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">*</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="p">);</span></span>
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888
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<pre style="margin: 0;">+<span id="LC888" class="line" lang="cpp"> <span class="n" style="color: #333;">memcpy</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">val_type</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;">i</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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889
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<pre style="margin: 0;">+<span id="LC889" class="line" lang="cpp"> <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="sc" style="color: #d14;">':'</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="890" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
890
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<pre style="margin: 0;">+<span id="LC890" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">val_type</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'c'</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">val_type</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'C'</span></span>
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<td class="diff-line-num new new_line" data-linenumber="891" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
891
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<pre style="margin: 0;">+<span id="LC891" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">val_type</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'i'</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">val_type</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'I'</span></span>
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<td class="diff-line-num new new_line" data-linenumber="892" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
892
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<pre style="margin: 0;">+<span id="LC892" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">val_type</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'s'</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">val_type</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'S'</span><span class="p">)</span> <span class="p">{</span></span>
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893
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<pre style="margin: 0;">+<span id="LC893" class="line" lang="cpp"> <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="sc" style="color: #d14;">'i'</span><span class="p">);</span></span>
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894
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<pre style="margin: 0;">+<span id="LC894" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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895
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<pre style="margin: 0;">+<span id="LC895" class="line" lang="cpp"> <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">val_type</span><span class="p">);</span></span>
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896
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<pre style="margin: 0;">+<span id="LC896" class="line" lang="cpp"> <span class="p">}</span></span>
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897
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<pre style="margin: 0;">+<span id="LC897" class="line" lang="cpp"> <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="sc" style="color: #d14;">':'</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;">i</span> <span class="o" style="font-weight: 600;">+=</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="p">);</span></span>
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899
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<pre style="margin: 0;">+<span id="LC899" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">switch</span> <span class="p">(</span><span class="n" style="color: #333;">val_type</span><span class="p">)</span> <span class="p">{</span></span>
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900
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<pre style="margin: 0;">+<span id="LC900" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'A'</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="901" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
901
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<pre style="margin: 0;">+<span id="LC901" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">A_val</span><span class="p">;</span></span>
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902
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<pre style="margin: 0;">+<span id="LC902" class="line" lang="cpp"> <span class="n" style="color: #333;">memcpy</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">A_val</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;">i</span><span class="p">,</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">A_val</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;">i</span> <span class="o" style="font-weight: 600;">+=</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">A_val</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="904" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
904
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<pre style="margin: 0;">+<span id="LC904" class="line" lang="cpp"> <span class="n" style="color: #333;">itoa10</span><span class="o" style="font-weight: 600;"><</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="n" style="color: #333;">A_val</span><span class="p">,</span> <span class="n" style="color: #333;">buf</span><span class="p">);</span></span>
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905
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<pre style="margin: 0;">+<span id="LC905" class="line" lang="cpp"> <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">buf</span><span class="p">);</span></span>
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906
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<pre style="margin: 0;">+<span id="LC906" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</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="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'c'</span><span class="p">:</span></span>
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908
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<pre style="margin: 0;">+<span id="LC908" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int8_t</span> <span class="n" style="color: #333;">c_val</span><span class="p">;</span></span>
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909
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<pre style="margin: 0;">+<span id="LC909" 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;">c_val</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;">i</span><span class="p">,</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">c_val</span><span class="p">));</span></span>
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910
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<pre style="margin: 0;">+<span id="LC910" class="line" lang="cpp"> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">+=</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">c_val</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="911" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
911
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<pre style="margin: 0;">+<span id="LC911" class="line" lang="cpp"> <span class="n" style="color: #333;">itoa10</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int8_t</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="n" style="color: #333;">c_val</span><span class="p">,</span> <span class="n" style="color: #333;">buf</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="912" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
912
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<pre style="margin: 0;">+<span id="LC912" class="line" lang="cpp"> <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">buf</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="913" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
913
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<pre style="margin: 0;">+<span id="LC913" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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914
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<pre style="margin: 0;">+<span id="LC914" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'C'</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="915" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
915
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<pre style="margin: 0;">+<span id="LC915" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint8_t</span> <span class="n" style="color: #333;">C_val</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="916" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
916
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<pre style="margin: 0;">+<span id="LC916" class="line" lang="cpp"> <span class="n" style="color: #333;">memcpy</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">C_val</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;">i</span><span class="p">,</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">C_val</span><span class="p">));</span></span>
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917
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<pre style="margin: 0;">+<span id="LC917" class="line" lang="cpp"> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">+=</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">C_val</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="918" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
918
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<pre style="margin: 0;">+<span id="LC918" class="line" lang="cpp"> <span class="n" style="color: #333;">itoa10</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">uint8_t</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="n" style="color: #333;">C_val</span><span class="p">,</span> <span class="n" style="color: #333;">buf</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="919" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
919
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<pre style="margin: 0;">+<span id="LC919" class="line" lang="cpp"> <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">buf</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="920" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
920
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<pre style="margin: 0;">+<span id="LC920" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="921" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
921
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<pre style="margin: 0;">+<span id="LC921" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'s'</span><span class="p">:</span></span>
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<td class="diff-line-num new old_line" data-linenumber="876" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="922" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
922
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<pre style="margin: 0;">+<span id="LC922" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int16_t</span> <span class="n" style="color: #333;">s_val</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="923" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
923
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<pre style="margin: 0;">+<span id="LC923" 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;">s_val</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;">i</span><span class="p">,</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">s_val</span><span class="p">));</span></span>
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<td class="diff-line-num new new_line" data-linenumber="924" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
924
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<pre style="margin: 0;">+<span id="LC924" class="line" lang="cpp"> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">+=</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">s_val</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="925" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
925
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<pre style="margin: 0;">+<span id="LC925" class="line" lang="cpp"> <span class="n" style="color: #333;">itoa10</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int16_t</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="n" style="color: #333;">s_val</span><span class="p">,</span> <span class="n" style="color: #333;">buf</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="926" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
926
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<pre style="margin: 0;">+<span id="LC926" class="line" lang="cpp"> <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">buf</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="927" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
927
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<pre style="margin: 0;">+<span id="LC927" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="928" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
928
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<pre style="margin: 0;">+<span id="LC928" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'S'</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="929" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
929
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<pre style="margin: 0;">+<span id="LC929" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint16_t</span> <span class="n" style="color: #333;">S_val</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="930" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
930
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<pre style="margin: 0;">+<span id="LC930" class="line" lang="cpp"> <span class="n" style="color: #333;">memcpy</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">S_val</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;">i</span><span class="p">,</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">S_val</span><span class="p">));</span></span>
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<td class="diff-line-num new new_line" data-linenumber="931" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
931
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<pre style="margin: 0;">+<span id="LC931" class="line" lang="cpp"> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">+=</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">S_val</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="932" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
932
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<pre style="margin: 0;">+<span id="LC932" class="line" lang="cpp"> <span class="n" style="color: #333;">itoa10</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">uint16_t</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="n" style="color: #333;">S_val</span><span class="p">,</span> <span class="n" style="color: #333;">buf</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="933" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
933
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<pre style="margin: 0;">+<span id="LC933" class="line" lang="cpp"> <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">buf</span><span class="p">);</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="934" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
934
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<pre style="margin: 0;">+<span id="LC934" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="935" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
935
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<pre style="margin: 0;">+<span id="LC935" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'i'</span><span class="p">:</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="936" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
936
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<pre style="margin: 0;">+<span id="LC936" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">i_val</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="937" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
937
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<pre style="margin: 0;">+<span id="LC937" class="line" lang="cpp"> <span class="n" style="color: #333;">memcpy</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">i_val</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;">i</span><span class="p">,</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">i_val</span><span class="p">));</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="938" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
938
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<pre style="margin: 0;">+<span id="LC938" class="line" lang="cpp"> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">+=</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">i_val</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="939" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
939
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<pre style="margin: 0;">+<span id="LC939" class="line" lang="cpp"> <span class="n" style="color: #333;">itoa10</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int32_t</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="n" style="color: #333;">i_val</span><span class="p">,</span> <span class="n" style="color: #333;">buf</span><span class="p">);</span></span>
</pre>
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940
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<pre style="margin: 0;">+<span id="LC940" class="line" lang="cpp"> <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">buf</span><span class="p">);</span></span>
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941
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<pre style="margin: 0;">+<span id="LC941" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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942
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<pre style="margin: 0;">+<span id="LC942" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'I'</span><span class="p">:</span></span>
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943
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<pre style="margin: 0;">+<span id="LC943" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">I_val</span><span class="p">;</span></span>
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944
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<pre style="margin: 0;">+<span id="LC944" class="line" lang="cpp"> <span class="n" style="color: #333;">memcpy</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">I_val</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;">i</span><span class="p">,</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">I_val</span><span class="p">));</span></span>
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<td class="diff-line-num new new_line" data-linenumber="945" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
945
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<pre style="margin: 0;">+<span id="LC945" class="line" lang="cpp"> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">+=</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">I_val</span><span class="p">);</span></span>
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946
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<pre style="margin: 0;">+<span id="LC946" class="line" lang="cpp"> <span class="n" style="color: #333;">itoa10</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="n" style="color: #333;">I_val</span><span class="p">,</span> <span class="n" style="color: #333;">buf</span><span class="p">);</span></span>
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947
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<pre style="margin: 0;">+<span id="LC947" class="line" lang="cpp"> <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">buf</span><span class="p">);</span></span>
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948
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<pre style="margin: 0;">+<span id="LC948" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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949
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<pre style="margin: 0;">+<span id="LC949" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'Z'</span><span class="p">:</span></span>
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950
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<pre style="margin: 0;">+<span id="LC950" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">c</span><span class="p">;</span></span>
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951
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<pre style="margin: 0;">+<span id="LC951" class="line" lang="cpp"> <span class="n" style="color: #333;">memcpy</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;">b</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="p">));</span></span>
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952
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<pre style="margin: 0;">+<span id="LC952" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">!=</span> <span class="sc" style="color: #d14;">'\0'</span><span class="p">)</span> <span class="p">{</span></span>
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953
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<pre style="margin: 0;">+<span id="LC953" class="line" lang="cpp"> <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">);</span></span>
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954
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<pre style="margin: 0;">+<span id="LC954" class="line" lang="cpp"> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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955
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<pre style="margin: 0;">+<span id="LC955" class="line" lang="cpp"> <span class="n" style="color: #333;">memcpy</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;">b</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</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="p">}</span></span>
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957
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<pre style="margin: 0;">+<span id="LC957" class="line" lang="cpp"> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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958
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<pre style="margin: 0;">+<span id="LC958" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC959" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">default</span><span class="o" style="font-weight: 600;">:</span></span>
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960
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<pre style="margin: 0;">+<span id="LC960" class="line" lang="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="LC961" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC962" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC963" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC964" class="line" lang="cpp"><span class="p">}</span></span></pre>
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<a href="https://salsa.debian.org/med-team/bowtie2/commit/157dbc209f47672a9a7167d16e3a324803906000#7398ca21ea2a2c7a38ca176ea1edaeb67b9ca8c0"><strong>sam.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">@@ -305,6 +305,11 @@ public:</td>
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<pre style="margin: 0;"> <span id="LC305" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">PerReadMetrics</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">prm</span><span class="p">,</span> <span class="c1" style="color: #998; font-style: italic;">// per-read metrics</span></span>
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306
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<pre style="margin: 0;"> <span id="LC306" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Scoring</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">sc</span><span class="p">)</span> <span class="c1" style="color: #998; font-style: italic;">// scoring scheme</span></span>
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<pre style="margin: 0;"> <span id="LC307" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC308" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC309" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">+<span id="LC310" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * Print optional flags that that have been preserve from BAM input</span></span>
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<pre style="margin: 0;">+<span id="LC311" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">+<span id="LC312" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">printPreservedOptFlags</span><span class="p">(</span><span class="n" style="color: #333;">BTString</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">o</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Read</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">rd</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="LC313" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC314" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;"> <span id="LC315" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * Return true iff we should try to obey the SAM spec's recommendations</span></span>
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<a href="https://salsa.debian.org/med-team/bowtie2/commit/157dbc209f47672a9a7167d16e3a324803906000#54bdc2e95dbd86d93a56d1f6445a8c2f9c6bedfb"><strong>scripts/test/simple_tests.pl</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">@@ -133,8 +133,23 @@ my @cases = (</td>
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<pre style="margin: 0;"> <span id="LC133" class="line" lang="perl"></span>
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<pre style="margin: 0;"> <span id="LC134" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># -c</span></span>
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<pre style="margin: 0;"> <span id="LC135" class="line" lang="perl"></span>
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="perl"> <span class="p">{</span> <span class="nv" style="color: teal;">name</span> <span class="o" style="font-weight: 600;">=></span> <span class="s" style="color: #d14;">"Align should not fail when first seq in ref is all Ns"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">ref</span> <span class="o" style="font-weight: 600;">=></span> <span class="p">[</span> <span class="s" style="color: #d14;">"NNNNNNNNNNNNNNN"</span><span class="p">,</span> <span class="s" style="color: #d14;">"AGCATCGATCAGTATCTGA"</span> <span class="p">],</span></span>
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="perl"> <span class="nv" style="color: teal;">cline_reads</span> <span class="o" style="font-weight: 600;">=></span> <span class="s" style="color: #d14;">"CATCGATCAGTATCTG"</span><span class="p">,</span></span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="perl"> <span class="nv" style="color: teal;">hits</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="mi" style="color: #099;">1</span> <span class="p">}]</span> <span class="p">},</span></span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="perl"></span>
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<td class="diff-line-num new new_line" data-linenumber="141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="perl"> <span class="p">{</span> <span class="nv" style="color: teal;">name</span> <span class="o" style="font-weight: 600;">=></span> <span class="s" style="color: #d14;">"Align should not fail when multiple seqs are all Ns"</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="142" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">ref</span> <span class="o" style="font-weight: 600;">=></span> <span class="p">[</span> <span class="s" style="color: #d14;">"NNNNNNNNNNNNNNN"</span><span class="p">,</span> <span class="s" style="color: #d14;">"NNNNNNNNNNNNNNN"</span><span class="p">,</span> <span class="s" style="color: #d14;">"AGCATCGATCAGTATCTGA"</span> <span class="p">],</span></span>
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143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="perl"> <span class="nv" style="color: teal;">cline_reads</span> <span class="o" style="font-weight: 600;">=></span> <span class="s" style="color: #d14;">"CATCGATCAGTATCTG"</span><span class="p">,</span></span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="perl"> <span class="nv" style="color: teal;">hits</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="mi" style="color: #099;">1</span> <span class="p">}]</span> <span class="p">},</span></span>
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145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="perl"></span>
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146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="perl"> <span class="p">{</span> <span class="nv" style="color: teal;">name</span> <span class="o" style="font-weight: 600;">=></span> <span class="s" style="color: #d14;">"Should account for stretch of Ns at beginning"</span><span class="p">,</span></span>
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147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">ref</span> <span class="o" style="font-weight: 600;">=></span> <span class="p">[</span> <span class="s" style="color: #d14;">"NNNNNNNNNNNNNNNAGCATCGATCAGTATCTGA"</span> <span class="p">],</span></span>
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148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="perl"> <span class="nv" style="color: teal;">cline_reads</span> <span class="o" style="font-weight: 600;">=></span> <span class="s" style="color: #d14;">"CATCGATCAGTATCTG"</span><span class="p">,</span></span>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="perl"> <span class="nv" style="color: teal;">hits</span> <span class="o" style="font-weight: 600;">=></span> <span class="p">[{</span> <span class="mi" style="color: #099;">17</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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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="perl"></span>
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136
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151
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<pre style="margin: 0;"> <span id="LC151" class="line" lang="perl"> <span class="p">{</span> <span class="nv" style="color: teal;">name</span> <span class="o" style="font-weight: 600;">=></span> <span class="s" style="color: #d14;">"Cline 1"</span><span class="p">,</span></span>
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137
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<pre style="margin: 0;">-<span id="LC137" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">ref</span> <span class="o" style="font-weight: 600;">=></span> <span class="p">[</span><span class="idiff left right"> </span><span class="s" style="color: #d14;">"AGCATCGATCAGTATCTGA"</span> <span class="p">],</span></span>
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152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">ref</span> <span class="o" style="font-weight: 600;">=></span> <span class="p">[</span><span class="s" style="color: #d14;">"AGCATCGATCAGTATCTGA"</span> <span class="p">],</span></span>
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138
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153
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<pre style="margin: 0;"> <span id="LC153" class="line" lang="perl"> <span class="nv" style="color: teal;">cline_reads</span> <span class="o" style="font-weight: 600;">=></span> <span class="s" style="color: #d14;">"CATCGATCAGTATCTG"</span><span class="p">,</span></span>
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139
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154
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<pre style="margin: 0;"> <span id="LC154" class="line" lang="perl"> <span class="nv" style="color: teal;">hits</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="mi" style="color: #099;">1</span> <span class="p">}]</span> <span class="p">},</span></span>
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140
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155
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<pre style="margin: 0;"> <span id="LC155" class="line" lang="perl"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="158" style="width: 35px; color: rgba(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="173" style="width: 35px; color: rgba(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">@@ -158,6 +173,41 @@ my @cases = (</td>
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158
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173
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<pre style="margin: 0;"> <span id="LC173" class="line" lang="perl"> <span class="nv" style="color: teal;">cline_reads</span> <span class="o" style="font-weight: 600;">=></span> <span class="s" style="color: #d14;">"CATCGATCAGTATCTG:ABCDEDGHIJKLMNOPQ"</span><span class="p">,</span> <span class="c1" style="color: #998; font-style: italic;"># qual too long</span></span>
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159
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174
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<pre style="margin: 0;"> <span id="LC174" class="line" lang="perl"> <span class="nv" style="color: teal;">should_abort</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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160
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175
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<pre style="margin: 0;"> <span id="LC175" class="line" lang="perl"></span>
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176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="perl"> <span class="p">{</span> <span class="nv" style="color: teal;">name</span> <span class="o" style="font-weight: 600;">=></span> <span class="s" style="color: #d14;">"trim-to: trim from 5'-end"</span><span class="p">,</span></span>
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177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">ref</span> <span class="o" style="font-weight: 600;">=></span> <span class="p">[</span> <span class="s" style="color: #d14;">"AGCATCGATCAGTATCTGA"</span> <span class="p">],</span></span>
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178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="perl"> <span class="nv" style="color: teal;">cline_reads</span> <span class="o" style="font-weight: 600;">=></span> <span class="s" style="color: #d14;">"CATCGATCAGTATCTG:IIIIIIIIIIIIIIII\n"</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="179" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="perl"> <span class="nv" style="color: teal;">args</span> <span class="o" style="font-weight: 600;">=></span> <span class="s" style="color: #d14;">"--trim-to 5:12"</span><span class="p">,</span></span>
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180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="perl"> <span class="nv" style="color: teal;">norc</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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181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="perl"> <span class="nv" style="color: teal;">hits</span> <span class="o" style="font-weight: 600;">=></span> <span class="p">[{</span> <span class="mi" style="color: #099;">6</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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182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="perl"></span>
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183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="perl"> <span class="p">{</span> <span class="nv" style="color: teal;">name</span> <span class="o" style="font-weight: 600;">=></span> <span class="s" style="color: #d14;">"trim-to: trim from 3'-end"</span><span class="p">,</span></span>
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184
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">ref</span> <span class="o" style="font-weight: 600;">=></span> <span class="p">[</span> <span class="s" style="color: #d14;">"AGCATCGATCAGTATCTGA"</span> <span class="p">],</span></span>
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185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="perl"> <span class="nv" style="color: teal;">cline_reads</span> <span class="o" style="font-weight: 600;">=></span> <span class="s" style="color: #d14;">"CATCGATCAGTATCTG:IIIIIIIIIIIIIIII\n"</span><span class="p">,</span></span>
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186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="perl"> <span class="nv" style="color: teal;">args</span> <span class="o" style="font-weight: 600;">=></span> <span class="s" style="color: #d14;">"--trim-to 3:12"</span><span class="p">,</span></span>
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187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="perl"> <span class="nv" style="color: teal;">norc</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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188
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="perl"> <span class="nv" style="color: teal;">hits</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="mi" style="color: #099;">1</span> <span class="p">}]</span> <span class="p">},</span></span>
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189
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="perl"></span>
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<td class="diff-line-num new new_line" data-linenumber="190" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
190
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="perl"> <span class="p">{</span> <span class="nv" style="color: teal;">name</span> <span class="o" style="font-weight: 600;">=></span> <span class="s" style="color: #d14;">"trim-to: trim from 3'-end (default)"</span><span class="p">,</span></span>
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191
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">ref</span> <span class="o" style="font-weight: 600;">=></span> <span class="p">[</span> <span class="s" style="color: #d14;">"AGCATCGATCAGTATCTGA"</span> <span class="p">],</span></span>
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192
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="perl"> <span class="nv" style="color: teal;">cline_reads</span> <span class="o" style="font-weight: 600;">=></span> <span class="s" style="color: #d14;">"CATCGATCAGTATCTG:IIIIIIIIIIIIIIII\n"</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" 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="perl"> <span class="nv" style="color: teal;">args</span> <span class="o" style="font-weight: 600;">=></span> <span class="s" style="color: #d14;">"--trim-to 12"</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="194" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
194
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="perl"> <span class="nv" style="color: teal;">norc</span> <span class="o" style="font-weight: 600;">=></span> <span class="mi" style="color: #099;">1</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="195" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
195
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="perl"> <span class="nv" style="color: teal;">hits</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="mi" style="color: #099;">1</span> <span class="p">}]</span> <span class="p">},</span></span>
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196
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="perl"></span>
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197
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="perl"> <span class="p">{</span> <span class="nv" style="color: teal;">name</span> <span class="o" style="font-weight: 600;">=></span> <span class="s" style="color: #d14;">"trim-to: invalid position"</span><span class="p">,</span></span>
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198
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">ref</span> <span class="o" style="font-weight: 600;">=></span> <span class="p">[</span> <span class="s" style="color: #d14;">"AGCATCGATCAGTATCTGA"</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="perl"> <span class="nv" style="color: teal;">cline_reads</span> <span class="o" style="font-weight: 600;">=></span> <span class="s" style="color: #d14;">"CATCGATCAGTATCTG:IIIIIIIIIIIIIIII\n"</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="perl"> <span class="nv" style="color: teal;">args</span> <span class="o" style="font-weight: 600;">=></span> <span class="s" style="color: #d14;">"--trim-to 4:12"</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="201" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
201
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="perl"> <span class="nv" style="color: teal;">norc</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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202
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="perl"> <span class="nv" style="color: teal;">should_abort</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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203
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="perl"></span>
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204
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="perl"> <span class="p">{</span> <span class="nv" style="color: teal;">name</span> <span class="o" style="font-weight: 600;">=></span> <span class="s" style="color: #d14;">"trim-to: invalid count"</span><span class="p">,</span></span>
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205
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">ref</span> <span class="o" style="font-weight: 600;">=></span> <span class="p">[</span> <span class="s" style="color: #d14;">"AGCATCGATCAGTATCTGA"</span> <span class="p">],</span></span>
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206
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="perl"> <span class="nv" style="color: teal;">cline_reads</span> <span class="o" style="font-weight: 600;">=></span> <span class="s" style="color: #d14;">"CATCGATCAGTATCTG:IIIIIIIIIIIIIIII\n"</span><span class="p">,</span></span>
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207
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="perl"> <span class="nv" style="color: teal;">args</span> <span class="o" style="font-weight: 600;">=></span> <span class="s" style="color: #d14;">"--trim-to 5:-12"</span><span class="p">,</span></span>
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208
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="perl"> <span class="nv" style="color: teal;">norc</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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209
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="perl"> <span class="nv" style="color: teal;">should_abort</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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210
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="perl"></span>
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161
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211
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<pre style="margin: 0;"> <span id="LC211" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># Part of sequence is trimmed</span></span>
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162
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212
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<pre style="margin: 0;"> <span id="LC212" class="line" lang="perl"> <span class="p">{</span> <span class="nv" style="color: teal;">name</span> <span class="o" style="font-weight: 600;">=></span> <span class="s" style="color: #d14;">"Cline 7"</span><span class="p">,</span></span>
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163
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213
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<pre style="margin: 0;"> <span id="LC213" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">ref</span> <span class="o" style="font-weight: 600;">=></span> <span class="p">[</span> <span class="s" style="color: #d14;">"AGCATCGATCAGTATCTGA"</span> <span class="p">],</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4518" style="width: 35px; color: rgba(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="4568" style="width: 35px; color: rgba(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">@@ -4518,7 +4568,7 @@ my $idx_type = "";</td>
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4518
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4568
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<pre style="margin: 0;"> <span id="LC4568" class="line" lang="perl"> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="4519" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4519
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4569
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<pre style="margin: 0;"> <span id="LC4569" class="line" lang="perl"> <span class="nv" style="color: teal;">$binary_type</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"--"</span> <span class="o" style="font-weight: 600;">.</span> <span class="nv" style="color: teal;">$binary_type</span><span class="p">;</span></span>
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4520
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4570
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<pre style="margin: 0;"> <span id="LC4570" class="line" lang="perl"> <span class="p">}</span></span>
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4521
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<pre style="margin: 0;">-<span id="LC4521" class="line" lang="perl"><span class="idiff left right"> </span></span>
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4571
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<pre style="margin: 0;">+<span id="LC4571" class="line" lang="perl"></span>
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<td class="diff-line-num old_line" data-linenumber="4522" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4522
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<td class="diff-line-num new_line" data-linenumber="4572" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4572
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<pre style="margin: 0;"> <span id="LC4572" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$cmd</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="4523" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4523
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<td class="diff-line-num new_line" data-linenumber="4573" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4573
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<pre style="margin: 0;"> <span id="LC4573" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$batch_size</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="nb" style="color: #0086b3;">rand</span><span class="p">(</span><span class="mi" style="color: #099;">16</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="4524" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4524
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<td class="diff-line-num new_line" data-linenumber="4574" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4574
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<pre style="margin: 0;"> <span id="LC4574" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: teal;">$pe</span><span class="p">)</span> <span class="p">{</span></span>
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