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<h3>
Andreas Tille 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/cf277464ee949fe563ca814a827b2387be02dbd1">cf277464</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2022-02-17T16:38:51+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2.4.5</pre>
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</ul>
<h4>28 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#7e43d6808132163da1c92d84bb5c6a900737fe4b">
.github/workflows/bowtie2.yml
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</li>
<li class="file-stats">
<a href="#dea7d9d2c0ed0c505374f9f90877bedd8f077710">
BOWTIE2_VERSION
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<li class="file-stats">
<a href="#f11fb3bba37e7060bedcd5895812b7c511c52651">
MANUAL
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</li>
<li class="file-stats">
<a href="#465370da702349b6dcb3f9f2026872cad6877efa">
MANUAL.markdown
</a>
</li>
<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="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
README.md
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<li class="file-stats">
<a href="#a177c5447e9cdcbfd7d1dc1c7140293d0cfbc779">
aligner_seed.cpp
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<li class="file-stats">
<a href="#c9b466ab26199558112972a17a75b8c21ac85c19">
aligner_seed.h
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<li class="file-stats">
<a href="#057e0784d807c7b84958635ddeeb5003f2751ece">
aln_sink.cpp
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<li class="file-stats">
<a href="#03d5fe68cb76a542cb9c06b8e03093e21319ca35">
blockwise_sa.h
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<li class="file-stats">
<a href="#464ce98392db4e108605b7a12696e7c3434eaf56">
bowtie2-build
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<li class="file-stats">
<a href="#999fd61d6ccb4c3bc242370d11e9095438b9e1d1">
bt2_build.cpp
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<li class="file-stats">
<a href="#d1904db8401bf0137951f60c3d4a34a7cf8e2e84">
bt2_idx.h
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<li class="file-stats">
<a href="#8900eca5df34d74c6e0548d5c00714f6e70c5a77">
bt2_inspect.cpp
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<li class="file-stats">
<a href="#64f1aac6be9dd64453121ce3592c43407e567ded">
bt2_io.cpp
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<li class="file-stats">
<a href="#9f15b0fe50d277c8d231ce47c6a42a8355f51ff0">
diff_sample.h
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<li class="file-stats">
<a href="#ccc364c6c660e798a4f3c3b78119cbea257aee1e">
doc/manual.html
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<li class="file-stats">
<a href="#a1ba375e8deab5b12b1347797835e927dca95425">
doc/website/manual.ssi
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<li class="file-stats">
<a href="#9485aa1b2c39982f48264019fde0712132ed80f5">
doc/website/recent_news.ssi
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<li class="file-stats">
<a href="#59bf596910fb7006481a4d8a45de81ff2bd75a4d">
doc/website/rhsidebar.ssi
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<li class="file-stats">
<a href="#7c4ae52e4a13c990d16c9530fb874ed79064a5cd">
pat.cpp
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<li class="file-stats">
<a href="#6c8922e214bc665a49b5acea11b505cbd36446c5">
pat.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="#c1e31d3892dc5f604d89ce46343574400583f46f">
reference.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="#3ec76e53f41bf5d12b7091741f12b8f2960bea2f">
<span class="new-file">
+
threadpool.h
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</a>
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<h4>Changes:</h4>
<li id="7e43d6808132163da1c92d84bb5c6a900737fe4b">
<a href="https://salsa.debian.org/med-team/bowtie2/-/commit/cf277464ee949fe563ca814a827b2387be02dbd1#7e43d6808132163da1c92d84bb5c6a900737fe4b"><strong>.github/workflows/bowtie2.yml</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="yaml"><span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">Basic compile and test on Ubuntu and MacOS</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="yaml"><span class="na" style="color: #008080;">on</span><span class="pi">:</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="yaml"> <span class="na" style="color: #008080;">push</span><span class="pi">:</span></span>
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<td class="new_line diff-line-num old" data-linenumber="4" 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="LC4" class="line" lang="yaml"> <span class="na" style="color: #008080;">branches</span><span class="pi">:</span> <span class="pi">[</span> <span class="nv" style="color: #008080;">bug_fixes master</span> <span class="pi">]</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="yaml"> <span class="na" style="color: #008080;">branches</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="yaml"> <span class="pi">-</span> <span class="s1" style="color: #d14;">'</span><span class="s" style="color: #d14;">bug_fixes'</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="yaml"> <span class="pi">-</span> <span class="s1" style="color: #d14;">'</span><span class="s" style="color: #d14;">master'</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="yaml"> <span class="na" style="color: #008080;">paths</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="yaml"> <span class="pi">-</span> <span class="s1" style="color: #d14;">'</span><span class="s" style="color: #d14;">**.h'</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="yaml"> <span class="pi">-</span> <span class="s1" style="color: #d14;">'</span><span class="s" style="color: #d14;">**.cpp'</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="yaml"> <span class="pi">-</span> <span class="s1" style="color: #d14;">'</span><span class="s" style="color: #d14;">bowtie2'</span></span>
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<td class="new_line diff-line-num new" 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="yaml"> <span class="pi">-</span> <span class="s1" style="color: #d14;">'</span><span class="s" style="color: #d14;">bowtie2-build'</span></span>
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<td class="new_line diff-line-num new" 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="yaml"> <span class="pi">-</span> <span class="s1" style="color: #d14;">'</span><span class="s" style="color: #d14;">bowtie2-inspect'</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="yaml"> <span class="pi">-</span> <span class="s1" style="color: #d14;">'</span><span class="s" style="color: #d14;">Makefile'</span></span>
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<td class="new_line diff-line-num new" 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="yaml"> <span class="pi">-</span> <span class="s1" style="color: #d14;">'</span><span class="s" style="color: #d14;">scripts/sim/**'</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="yaml"> <span class="pi">-</span> <span class="s1" style="color: #d14;">'</span><span class="s" style="color: #d14;">scripts/test/**'</span></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="yaml"> <span class="na" style="color: #008080;">pull_request</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="yaml"> <span class="na" style="color: #008080;">branches</span><span class="pi">:</span> <span class="pi">[</span> <span class="nv" style="color: #008080;">$default-branch</span> <span class="pi">]</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="yaml"> <span class="na" style="color: #008080;">branches</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="yaml"> <span class="pi">-</span> <span class="s1" style="color: #d14;">'</span><span class="s" style="color: #d14;">master'</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="yaml"> <span class="na" style="color: #008080;">paths</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="yaml"> <span class="pi">-</span> <span class="s1" style="color: #d14;">'</span><span class="s" style="color: #d14;">**.h'</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="yaml"> <span class="pi">-</span> <span class="s1" style="color: #d14;">'</span><span class="s" style="color: #d14;">**.cpp'</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="yaml"> <span class="pi">-</span> <span class="s1" style="color: #d14;">'</span><span class="s" style="color: #d14;">bowtie2'</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="yaml"> <span class="pi">-</span> <span class="s1" style="color: #d14;">'</span><span class="s" style="color: #d14;">bowtie2-build'</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="yaml"> <span class="pi">-</span> <span class="s1" style="color: #d14;">'</span><span class="s" style="color: #d14;">bowtie2-inspect'</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="yaml"> <span class="pi">-</span> <span class="s1" style="color: #d14;">'</span><span class="s" style="color: #d14;">Makefile'</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="yaml"> <span class="pi">-</span> <span class="s1" style="color: #d14;">'</span><span class="s" style="color: #d14;">scripts/sim/**'</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="yaml"> <span class="pi">-</span> <span class="s1" style="color: #d14;">'</span><span class="s" style="color: #d14;">scripts/test/**'</span></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="yaml"><span class="na" style="color: #008080;">jobs</span><span class="pi">:</span></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="yaml"> <span class="na" style="color: #008080;">setup</span><span class="pi">:</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="yaml"> <span class="na" style="color: #008080;">runs-on</span><span class="pi">:</span> <span class="s" style="color: #d14;">ubuntu-latest</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -15,17 +36,20 @@ jobs:</td>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="yaml"> <span class="s" style="color: #d14;">sudo apt-get update</span></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="yaml"> <span class="s" style="color: #d14;">sudo apt-get install zlib1g-dev</span></span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="yaml"> <span class="na" style="color: #008080;">linux</span><span class="pi">:</span></span>
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18
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="yaml"> <span class="na" style="color: #008080;">needs</span><span class="pi">:</span> <span class="s" style="color: #d14;">setup</span></span>
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19
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="yaml"> <span class="na" style="color: #008080;">runs-on</span><span class="pi">:</span> <span class="s" style="color: #d14;">ubuntu-latest</span></span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="yaml"> <span class="na" style="color: #008080;">needs</span><span class="pi">:</span> <span class="s" style="color: #d14;">setup</span></span>
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20
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="yaml"> <span class="na" style="color: #008080;">steps</span><span class="pi">:</span></span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">uses</span><span class="pi">:</span> <span class="s" style="color: #d14;">actions/checkout@v2</span></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">run</span><span class="pi">:</span> <span class="pi">|</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">Run simple tests</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="yaml"> <span class="na" style="color: #008080;">run</span><span class="pi">:</span> <span class="pi">|</span></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="yaml"> <span class="s" style="color: #d14;">make allall</span></span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="yaml"> <span class="s" style="color: #d14;">make simple-test</span></span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="yaml"> <span class="na" style="color: #008080;">macos</span><span class="pi">:</span></span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="yaml"> <span class="na" style="color: #008080;">runs-on</span><span class="pi">:</span> <span class="s" style="color: #d14;">macos-latest</span></span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="yaml"> <span class="na" style="color: #008080;">steps</span><span class="pi">:</span></span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">uses</span><span class="pi">:</span> <span class="s" style="color: #d14;">actions/checkout@v2</span></span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">run</span><span class="pi">:</span> <span class="pi">|</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">Run simple tests</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="yaml"> <span class="na" style="color: #008080;">run</span><span class="pi">:</span> <span class="pi">|</span></span>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="yaml"> <span class="s" style="color: #d14;">make allall</span></span>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="yaml"> <span class="s" style="color: #d14;">make simple-test</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="yaml"> <span class="s" style="color: #d14;">make random-test</span></span></pre>
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<a href="https://salsa.debian.org/med-team/bowtie2/-/commit/cf277464ee949fe563ca814a827b2387be02dbd1#dea7d9d2c0ed0c505374f9f90877bedd8f077710"><strong>BOWTIE2_VERSION</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">2.4.4</span></pre>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">2.4.5</span></pre>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1924,6 +1924,10 @@ format:</td>
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<pre style="margin: 0;"> <span id="LC1924" class="line" lang="plaintext">Fields are separated by tabs. Colorspace is always set to 0 for Bowtie</span>
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<pre style="margin: 0;"> <span id="LC1925" class="line" lang="plaintext">2.</span>
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1926
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<pre style="margin: 0;"> <span id="LC1926" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC1927" class="line" lang="plaintext"> -o/--output <filename></span>
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1928
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<pre style="margin: 0;">+<span id="LC1928" class="line" lang="plaintext"></span>
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1929
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<pre style="margin: 0;">+<span id="LC1929" class="line" lang="plaintext">Save output to user-specified filename (default: stdout)</span>
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1930
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<pre style="margin: 0;">+<span id="LC1930" class="line" lang="plaintext"></span>
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1927
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1931
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<pre style="margin: 0;"> <span id="LC1931" class="line" lang="plaintext"> -v/--verbose</span>
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1928
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1932
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<pre style="margin: 0;"> <span id="LC1932" class="line" lang="plaintext"></span>
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1929
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1933
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<pre style="margin: 0;"> <span id="LC1933" class="line" lang="plaintext">Print verbose output (for debugging).</span>
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<br>
</li>
<li id="465370da702349b6dcb3f9f2026872cad6877efa">
<a href="https://salsa.debian.org/med-team/bowtie2/-/commit/cf277464ee949fe563ca814a827b2387be02dbd1#465370da702349b6dcb3f9f2026872cad6877efa"><strong>MANUAL.markdown</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2584" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -2584,6 +2584,14 @@ names and lengths of the input sequences. The summary has this format:</td>
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2584
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2584
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<pre style="margin: 0;"> <span id="LC2584" class="line" lang="markdown"></span>
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2585
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2585
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<pre style="margin: 0;"> <span id="LC2585" class="line" lang="markdown">Fields are separated by tabs. Colorspace is always set to 0 for Bowtie 2.</span>
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2586
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2586
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<pre style="margin: 0;"> <span id="LC2586" class="line" lang="markdown"></span>
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2587
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<pre style="margin: 0;">+<span id="LC2587" class="line" lang="markdown"><span class="nt" style="color: #000080;"></td></tr><tr><td</span> <span class="na" style="color: #008080;">id=</span><span class="s" style="color: #d14;">"bowtie2-inspect-options-o"</span><span class="nt" style="color: #000080;">></span></span>
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2588
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<pre style="margin: 0;">+<span id="LC2588" class="line" lang="markdown"></span>
</pre>
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2589
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<pre style="margin: 0;">+<span id="LC2589" class="line" lang="markdown"><span class="sb" style="color: #d14;"> -o/--output <filename></span></span>
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2590
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<pre style="margin: 0;">+<span id="LC2590" class="line" lang="markdown"></span>
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2591
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<pre style="margin: 0;">+<span id="LC2591" class="line" lang="markdown"><span class="nt" style="color: #000080;"></td><td></span></span>
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2592
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<pre style="margin: 0;">+<span id="LC2592" class="line" lang="markdown"></span>
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2593
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<pre style="margin: 0;">+<span id="LC2593" class="line" lang="markdown">Save output to user-specified filename (default: stdout)</span>
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2594
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<pre style="margin: 0;">+<span id="LC2594" class="line" lang="markdown"></span>
</pre>
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2587
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2595
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<pre style="margin: 0;"> <span id="LC2595" class="line" lang="markdown"><span class="nt" style="color: #000080;"></td></tr><tr><td></span></span>
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2588
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2596
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<pre style="margin: 0;"> <span id="LC2596" class="line" lang="markdown"></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="2589" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2589
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<td class="new_line diff-line-num" data-linenumber="2597" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2597
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<pre style="margin: 0;"> <span id="LC2597" class="line" lang="markdown"><span class="sb" style="color: #d14;"> -v/--verbose</span></span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2913" style="width: 35px; color: rgba(0,0,0,0.3); 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="2921" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -2913,6 +2921,7 @@ warnings due to the case insensitive nature of markdown URLs --></td>
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2913
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2921
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<pre style="margin: 0;"> <span id="LC2921" class="line" lang="markdown"><span class="p">[</span><span class="ss" style="color: #990073;">`-m`</span><span class="p">]:</span> <span class="sx" style="color: #d14;">#bowtie2-options-m</span></span>
</pre>
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2914
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2922
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<pre style="margin: 0;"> <span id="LC2922" class="line" lang="markdown"><span class="p">[</span><span class="ss" style="color: #990073;">`-n`/`--names`</span><span class="p">]:</span> <span class="sx" style="color: #d14;">#bowtie2-inspect-options-n</span></span>
</pre>
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2915
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<td class="new_line diff-line-num" data-linenumber="2923" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2923
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<pre style="margin: 0;"> <span id="LC2923" class="line" lang="markdown"><span class="p">[</span><span class="ss" style="color: #990073;">`-o`/`--offrate`</span><span class="p">]:</span> <span class="sx" style="color: #d14;">#bowtie2-options-o</span></span>
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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;">`-o`/`--output`</span><span class="p">]:</span> <span class="sx" style="color: #d14;">#bowtie2-inspect-options-o</span></span>
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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;">`-o`</span><span class="p">]:</span> <span class="sx" style="color: #d14;">#bowtie2-options-o</span></span>
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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;">`-p`/`--packed`</span><span class="p">]:</span> <span class="sx" style="color: #d14;">#bowtie2-build-options-p</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;">`-p`/`--threads`</span><span class="p">]:</span> <span class="sx" style="color: #d14;">#bowtie2-options-p</span></span>
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<a href="https://salsa.debian.org/med-team/bowtie2/-/commit/cf277464ee949fe563ca814a827b2387be02dbd1#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">@@ -43,6 +43,9 @@ ifneq (,$(findstring MINGW,$(shell uname)))</td>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="make"> <span class="nv" style="color: #008080;">WINDOWS</span> <span class="o" style="font-weight: 600;">:=</span> 1</span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="make"> <span class="nv" style="color: #008080;">MINGW</span> <span class="o" style="font-weight: 600;">:=</span> 1</span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="make"> <span class="c" style="color: #998; font-style: italic;"># POSIX memory-mapped files not currently supported on Windows</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="make"><span class="k" style="font-weight: 600;">endif</span></span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="make"></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="make"><span class="k" style="font-weight: 600;">ifeq</span> <span class="nv" style="color: #008080;">(1, $(WINDOWS))</span></span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="make"> <span class="nv" style="color: #008080;">BOWTIE_MM</span> <span class="o" style="font-weight: 600;">:=</span></span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="make"> <span class="nv" style="color: #008080;">BOWTIE_SHARED_MEM</span> <span class="o" style="font-weight: 600;">:=</span></span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="make"><span class="k" style="font-weight: 600;">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">@@ -252,7 +255,7 @@ GENERAL_LIST := $(wildcard scripts/*.sh) \</td>
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<pre style="margin: 0;"> <span id="LC255" class="line" lang="make"></span>
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<pre style="margin: 0;"> <span id="LC256" class="line" lang="make"><span class="k" style="font-weight: 600;">ifeq</span> <span class="nv" style="color: #008080;">(1,$(WINDOWS))</span></span>
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<pre style="margin: 0;"> <span id="LC257" class="line" lang="make"> <span class="nv" style="color: #008080;">BOWTIE2_BIN_LIST</span> <span class="o" style="font-weight: 600;">:=</span> <span class="nv" style="color: #008080;">$(BOWTIE2_BIN_LIST)</span> bowtie2.bat bowtie2-build.bat bowtie2-inspect.bat</span>
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<pre style="margin: 0;">-<span id="LC255" class="line" lang="make"> <span class="nv" style="color: #008080;">CXXFLAGS</span> <span class="o" style="font-weight: 600;">+=</span> <span class="nt" style="color: #000080;">-static-libgcc</span> <span class="nt" style="color: #000080;">-static-libstdc</span>++</span>
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<pre style="margin: 0;">+<span id="LC258" class="line" lang="make"> <span class="nv" style="color: #008080;">CXXFLAGS</span> <span class="o" style="font-weight: 600;">+=</span> <span class="nt" style="color: #000080;">-static-libgcc</span> <span class="nt" style="color: #000080;">-static-libstdc</span>++<span class="idiff left"> </span><span class="nt" style="color: #000080;"><span class="idiff right">-static</span></span></span>
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<pre style="margin: 0;"> <span id="LC259" class="line" lang="make"><span class="k" style="font-weight: 600;">endif</span></span>
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<pre style="margin: 0;"> <span id="LC260" class="line" lang="make"></span>
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<pre style="margin: 0;"> <span id="LC261" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># This is helpful on Windows under MinGW/MSYS, where Make might go for</span></span>
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<a href="https://salsa.debian.org/med-team/bowtie2/-/commit/cf277464ee949fe563ca814a827b2387be02dbd1#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">@@ -4,7 +4,7 @@ Bowtie 2 NEWS</td>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">Bowtie 2 is available for download from the project website,</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">http://bowtie-bio.sf.net/bowtie2 and on Github,</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">https://github.com/BenLangmead/bowtie2/releases. 2.0.0-beta1 is</span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext">the first version released to the public and 2.4.<span class="idiff left right">4</span> is the latest</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">the first version released to the public and 2.4.<span class="idiff left right">5</span> is the latest</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">version. Bowtie 2 is licensed under the GPLv3 license. See `LICENSE'</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">file for details.</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"></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">@@ -19,546 +19,612 @@ 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 2.4.<span class="idiff left">4</span> - <span class="idiff">May 23</span>, 202<span class="idiff right">1</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"><span class="idiff left">## </span>Version 2.4.<span class="idiff">5</span> - <span class="idiff">Jan 15</span>, 202<span class="idiff right">2 ##</span></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 an issue that would sometimes cause deadlocks in `bowtie2`</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">### bowtie2 ###</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"> * Fixed issues with `bowtie2` BAM parser that would cause `bowtie2` to</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext"> crash when processing input that was encoded with tools other than</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext"> samtools e.g. Picard.</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext"> * Fixed an issue causing `bowtie2` to drop certain optional fields when</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext"> when aligning BAM reads with the `--preserve-tags` option.</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext"> * Fixed an issue causing `bowtie2` to produce mangled SAM output when</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext"> specifying `--sam-append-comment` together with the `--passthrough`</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext"> option.</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext"> * Appended `GO:query` to SAM `@HD` entry to indicate that reads are</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext"> grouped by query name, bump SAM version to 1.5 to indicate support</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext"> for this change.</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext">### bowtie2-build ###</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext"> * Implemented thread pool to address performance regressions</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext"> introduced during the switch to C++11 threads.</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext"> * Fixed an issue causing masked-sequence metadata to be omitted</span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext"> from index. This issue would subsequently result in sequence</span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext"> data, `@SQ`, being left out from alignment SAM header.</span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext"> * Included `.tmp` extension to index files currenlty being built.</span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext"> The extension is removed only upon successful build. This change</span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext"> seeks to address the assumption that `bowtie2-build` ran successfully</span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext"> without building the reverse indexes.</span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext"> * Fixed an issue causing `bowtie2-build` to sometimes incorrectly</span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext"> calculate input size. This issue would result in the wrong index type</span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext"> being chosen and only happened with GZip compressed files.</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">### bowtie2-inspect ###</span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext"> * Added a new `-o/--output` option to save the output of</span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="plaintext"> `bowtie2-inspect` to a file instead of being dumped to standard</span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="plaintext"> output.</span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="plaintext">## Version 2.4.4 - May 23, 2021 ##</span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="plaintext"> * Fixed an issue that would sometimes cause deadlocks in `bowtie2`</span>
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25
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63
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="plaintext"> when running multithreaded</span>
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26
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64
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="plaintext"></span>
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27
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="plaintext">Version 2.4.3 - May 13, 2021</span>
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28
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="plaintext"></span>
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29
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="plaintext"><span class="idiff left right"> </span> * Replaced TBB concurrency with C++ threads</span>
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30
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="plaintext"><span class="idiff left right"> </span> * Added native support for processing Zstd-compressed read files</span>
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31
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="plaintext"> <span class="idiff left right"> </span>to bowtie2</span>
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32
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="plaintext"><span class="idiff left right"> </span> * Added native support for processing Zstd-compressed</span>
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33
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="plaintext"> <span class="idiff left right"> </span>reference-genome files to bowtie2-build</span>
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34
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="plaintext"><span class="idiff left right"> </span> * Fixed an issue causing `bowtie2` to report incorrect alignments</span>
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35
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="plaintext"> <span class="idiff left right"> </span>on big-endian machines</span>
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36
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="plaintext"><span class="idiff left right"> </span> * Fixed an issue causing `bowtie2` to incorrectly process BAM</span>
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37
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="plaintext"> <span class="idiff left right"> </span>files on big-endian machines</span>
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38
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="plaintext"><span class="idiff left right"> </span> * Fixed an issue causing Bowtie2 to set an incorrect MAPQ when AS and</span>
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39
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="plaintext"> <span class="idiff left right"> </span>XS are the maximum for read length</span>
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40
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="plaintext"><span class="idiff left right"> </span> * Add support for building on Apple M1 processors</span>
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41
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="plaintext"></span>
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42
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="plaintext">Version 2.4.2 - Oct 5, 2020</span>
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43
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="plaintext"></span>
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44
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="plaintext"><span class="idiff left right"> </span> * Fixed an issue that would cause the `bowtie2` wrapper script to throw</span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="plaintext"> <span class="idiff left right"> </span>an error when using wrapper-specific arguments.</span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="plaintext"><span class="idiff left right"> </span> * Added new `--sam-append-comment` flag that appends comment from FASTA/Q</span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="plaintext"> <span class="idiff left right"> </span>read to corresponding SAM record.</span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="plaintext"><span class="idiff left right"> </span> * Fixed an issue that would cause qupto, `-u`, to overflow when there</span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="plaintext"> <span class="idiff left right"> </span>are >= 2^32 query sequences (PR #312).</span>
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="plaintext"><span class="idiff left right"> </span> * Fixed an issue that would cause bowtie2-build script to incorrectly</span>
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="plaintext"> <span class="idiff left right"> </span>process reference files.</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">Version 2.4.1 - Feb 28, 2020</span>
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="plaintext"><span class="idiff left right"> </span> * Fixed an issue that would cause the `bowtie2` wrapper script to incorrectly</span>
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="plaintext"> <span class="idiff left right"> </span>process certain arguments.</span>
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="plaintext">Version 2.4.0 - Feb 25, 2020</span>
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="plaintext"><span class="idiff left right"> </span> * Fixed an issue in `-b <bam>` input mode where one might prematurely close the</span>
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="plaintext"> <span class="idiff left right"> </span>read file pointer causing "Bad file descriptor" in other threads</span>
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="plaintext"><span class="idiff left right"> </span> * Fixed an issue that could cause `bowtie2` to crash in `--no-1mm-upfront` mode</span>
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="plaintext"><span class="idiff left right"> </span> * Modified `bowtie2-build` to better handle of flags and positional parameters</span>
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="plaintext"><span class="idiff left right"> </span> * Migrated all `python` scripts to `python3`</span>
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="plaintext"><span class="idiff left right"> </span> * Added support for wildcards in input files to `bowtie2`, e.g. `bowtie2 -x</span>
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<pre style="margin: 0;">-<span id="LC66" class="line" lang="plaintext"> <span class="idiff left right"> </span>index -q *.fq` as opposed to `bowtie2 -x index -q 1.fq,2.fq,3.fq...`</span>
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67
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="plaintext"><span class="idiff left right"> </span> * Fixed an issue causing <code>bowtie2</code> to incorrectly process read names</span>
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68
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<pre style="margin: 0;">-<span id="LC68" class="line" lang="plaintext"> <span class="idiff left right"> </span>with slash mates plus extra characters (see</span>
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="plaintext"> <span class="idiff left right"> </span>[#265](https://github.com/BenLangmead/bowtie2/issues/265))</span>
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="plaintext"><span class="idiff left right"> </span> * Clarified support for overriding presets with more specific options e.g</span>
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="plaintext"> <span class="idiff left right"> </span>`bowtie2 -x index --local --very-fast-local --L22 -q reads.fq` will set the</span>
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72
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="plaintext"> <span class="idiff left right"> </span>seed length to 22, overriding the 25 set by `--very-fast-local`</span>
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73
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<pre style="margin: 0;">-<span id="LC73" class="line" lang="plaintext"><span class="idiff left right"> </span> * Modified SAM output for `-k`/`-a` so that supplementary alignments get</span>
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74
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<pre style="margin: 0;">-<span id="LC74" class="line" lang="plaintext"> <span class="idiff left right"> </span>assigned a MAPQ of 255</span>
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75
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<pre style="margin: 0;">-<span id="LC75" class="line" lang="plaintext"><span class="idiff left right"> </span> * Fixed an issue that would sometimes cause `bowtie2-build` to not generate</span>
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76
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<pre style="margin: 0;">-<span id="LC76" class="line" lang="plaintext"> <span class="idiff left right"> </span>reverse index files</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"> </span> * Added preliminary support for ppc64le architectures with the help of SIMDE</span>
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78
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<pre style="margin: 0;">-<span id="LC78" class="line" lang="plaintext"> <span class="idiff left right"> </span>project (see [#271](https://github.com/BenLangmead/bowtie2/issues/271))</span>
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79
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<pre style="margin: 0;">-<span id="LC79" class="line" lang="plaintext"><span class="idiff left right"> </span> * Fixed an issue causing `bowtie2` to incorrectly calculate the MAPQ when `--mp`</span>
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80
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<pre style="margin: 0;">-<span id="LC80" class="line" lang="plaintext"> <span class="idiff left right"> </span>was specified in combination with `--ignore-quals`</span>
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81
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<pre style="margin: 0;">-<span id="LC81" class="line" lang="plaintext"></span>
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82
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<pre style="margin: 0;">-<span id="LC82" class="line" lang="plaintext">Version 2.3.5.1 - Apr 16, 2019</span>
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83
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<pre style="margin: 0;">-<span id="LC83" class="line" lang="plaintext"></span>
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84
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<pre style="margin: 0;">-<span id="LC84" class="line" lang="plaintext"><span class="idiff left right"> </span> * Added official support for BAM input files</span>
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<td class="old_line diff-line-num old" data-linenumber="85" 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">
85
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<pre style="margin: 0;">-<span id="LC85" class="line" lang="plaintext"><span class="idiff left right"> </span> * Added official support for CMake build system</span>
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<td class="old_line diff-line-num old" data-linenumber="86" 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">
86
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<pre style="margin: 0;">-<span id="LC86" class="line" lang="plaintext"><span class="idiff left right"> </span> * Added changes to Makefile for creating Reproducible builds (via [210](https://github.com/BenLangmead/bowtie2/pull/210))</span>
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87
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<pre style="margin: 0;">-<span id="LC87" class="line" lang="plaintext"><span class="idiff left right"> </span> * Fix an issue whereby building on aarch64 would require patching sed commands (via [#243](https://github.com/BenLangmead/bowtie2/pull/243))</span>
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88
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<pre style="margin: 0;">-<span id="LC88" class="line" lang="plaintext"><span class="idiff left right"> </span> * Fix an issue whereby `bowtie2` would incorrectly throw an error while processing `--interleaved` input</span>
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89
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<pre style="margin: 0;">-<span id="LC89" class="line" lang="plaintext"></span>
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90
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<pre style="margin: 0;">-<span id="LC90" class="line" lang="plaintext">Version 2.3.5 - Mar 16, 2019</span>
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91
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<pre style="margin: 0;">-<span id="LC91" class="line" lang="plaintext"></span>
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92
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<pre style="margin: 0;">-<span id="LC92" class="line" lang="plaintext"><span class="idiff left right"> </span> * Added support for obtaining input reads directly from the Sequence Read Archive, via NCBI's [NGS language bindings](https://github.com/ncbi/ngs). This is activated via the [`--sra-acc`](manual.shtml#bowtie2-options-sra-acc) option. This implementation is based on Daehwan Kim's in [HISAT2](https://ccb.jhu.edu/software/hisat2). Supports both unpaired and paired-end inputs.</span>
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93
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<pre style="margin: 0;">-<span id="LC93" class="line" lang="plaintext"><span class="idiff left right"> </span> * Bowtie 2 now compiles on ARM architectures (via [#216](https://github.com/BenLangmead/bowtie2/pull/216))</span>
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94
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<pre style="margin: 0;">-<span id="LC94" class="line" lang="plaintext"><span class="idiff left right"> </span> * `--interleaved` can now be combined with FASTA inputs (worked only with FASTQ before)</span>
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<td class="old_line diff-line-num old" data-linenumber="95" 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">
95
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<pre style="margin: 0;">-<span id="LC95" class="line" lang="plaintext"><span class="idiff left right"> </span> * Fixed issue whereby large indexes were not successfully found in the `$BOWTIE2_INDEXES` directory</span>
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96
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<pre style="margin: 0;">-<span id="LC96" class="line" lang="plaintext"><span class="idiff left right"> </span> * Fixed input from FIFOs (e.g. via process substitution) to distinguish gzip-compressed versus uncompressed input</span>
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97
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<pre style="margin: 0;">-<span id="LC97" class="line" lang="plaintext"><span class="idiff left right"> </span> * Fixed issue whereby arguments containing `bz2` `lz4` were misinterpretted as files</span>
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98
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<pre style="margin: 0;">-<span id="LC98" class="line" lang="plaintext"><span class="idiff left right"> </span> * Fixed several compiler warnings</span>
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99
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<pre style="margin: 0;">-<span id="LC99" class="line" lang="plaintext"><span class="idiff left right"> </span> * Fixed issue whereby both ends of a paired-end read could have negative TLEN if they exactly coincided</span>
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100
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<pre style="margin: 0;">-<span id="LC100" class="line" lang="plaintext"><span class="idiff left right"> </span> * Fixed issue whereby `bowtie2-build` would hang on end-of-file (via [#228](https://github.com/BenLangmead/bowtie2/pull/228))</span>
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101
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<pre style="margin: 0;">-<span id="LC101" class="line" lang="plaintext"><span class="idiff left right"> </span> * Fixed issue whereby wrapper script would sometimes create zombie processes (via [#51](https://github.com/BenLangmead/bowtie2/pull/51))</span>
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102
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<pre style="margin: 0;">-<span id="LC102" class="line" lang="plaintext"><span class="idiff left right"> </span> * Fixed issue whereby `bowtie2-build` and `bowtie2-inspect` wrappers would fail on some versions of Python/PyPy</span>
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<td class="old_line diff-line-num old" data-linenumber="103" 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">
103
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<pre style="margin: 0;">-<span id="LC103" class="line" lang="plaintext"><span class="idiff left right"> </span> * Replaced old, unhelpful `README.md` in the project with a version that includes badges, links and some highlights from the manual</span>
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104
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<pre style="margin: 0;">-<span id="LC104" class="line" lang="plaintext"><span class="idiff left right"> </span> * Note: BAM input support and CMake build support both remain experimental, but we expect to finalize them in the next release</span>
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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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106
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<pre style="margin: 0;">-<span id="LC106" class="line" lang="plaintext">Version 2.3.4.3 - Sep 17, 2018</span>
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107
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<pre style="margin: 0;">-<span id="LC107" 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"><span class="idiff left right"> </span> * Fixed an issue causing `bowtie2-build` and `bowtie2-inspect`</span>
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<td class="old_line diff-line-num old" data-linenumber="109" 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">
109
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<pre style="margin: 0;">-<span id="LC109" class="line" lang="plaintext"> <span class="idiff left right"> </span>to output incomplete help text.</span>
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<td class="old_line diff-line-num old" data-linenumber="110" 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">
110
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<pre style="margin: 0;">-<span id="LC110" class="line" lang="plaintext"><span class="idiff left right"> </span> * Fixed an issue causing `bowtie2-inspect` to crash.</span>
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<td class="old_line diff-line-num old" data-linenumber="111" 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">
111
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<pre style="margin: 0;">-<span id="LC111" class="line" lang="plaintext"><span class="idiff left right"> </span> * Fixed an issue preventing `bowtie2` from processing paired and/or</span>
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<td class="old_line diff-line-num old" data-linenumber="112" 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">
112
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<pre style="margin: 0;">-<span id="LC112" class="line" lang="plaintext"> <span class="idiff left right"> </span>unpaired FASTQ reads together with interleaved FASTQ reads.</span>
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<td class="old_line diff-line-num old" data-linenumber="113" 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">
113
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<pre style="margin: 0;">-<span id="LC113" class="line" lang="plaintext"></span>
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114
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<pre style="margin: 0;">-<span id="LC114" class="line" lang="plaintext">Version 2.3.4.2 - Aug 7, 2018</span>
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115
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<pre style="margin: 0;">-<span id="LC115" 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"><span class="idiff left right"> </span> * Fixed issue causing `bowtie2` to fail in `--fast-local` mode.</span>
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<td class="old_line diff-line-num old" data-linenumber="117" 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">
117
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<pre style="margin: 0;">-<span id="LC117" class="line" lang="plaintext"><span class="idiff left right"> </span> * Fixed issue causing `--soft-clipped-unmapped-tlen` to be a positional argument.</span>
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<td class="old_line diff-line-num old" data-linenumber="118" 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">
118
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<pre style="margin: 0;">-<span id="LC118" class="line" lang="plaintext"><span class="idiff left right"> </span> * New option `--trim-to N` causes `bowtie2` to trim reads longer</span>
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<td class="old_line diff-line-num old" data-linenumber="119" 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">
119
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<pre style="margin: 0;">-<span id="LC119" class="line" lang="plaintext"> <span class="idiff left right"> </span>than `N` bases to exactly `N` bases. Can trim from either 3'</span>
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<td class="old_line diff-line-num old" data-linenumber="120" 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">
120
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<pre style="margin: 0;">-<span id="LC120" class="line" lang="plaintext"> <span class="idiff left right"> </span>or 5' end, e.g. `--trim-to 5:30` trims reads to 30 bases,</span>
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121
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<pre style="margin: 0;">-<span id="LC121" class="line" lang="plaintext"> <span class="idiff left right"> </span>truncating at the 5' end.</span>
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122
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<pre style="margin: 0;">-<span id="LC122" class="line" lang="plaintext"><span class="idiff left right"> </span> * Updated "Building from source" manual section with additional</span>
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123
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<pre style="margin: 0;">-<span id="LC123" class="line" lang="plaintext"> <span class="idiff left right"> </span>instructions on installing TBB.</span>
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124
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<pre style="margin: 0;">-<span id="LC124" class="line" lang="plaintext"><span class="idiff left right"> </span> * Several other updates to manual, including new mentions of</span>
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125
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<pre style="margin: 0;">-<span id="LC125" class="line" lang="plaintext"> <span class="idiff left right"> </span>[Bioconda](http://bioconda.github.io) and</span>
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126
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<pre style="margin: 0;">-<span id="LC126" class="line" lang="plaintext"> <span class="idiff left right"> </span>[Biocontainers](https://biocontainers.pro).</span>
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127
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<pre style="margin: 0;">-<span id="LC127" class="line" lang="plaintext"><span class="idiff left right"> </span> * Fixed an issue preventing `bowtie2` from processing more than</span>
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128
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<pre style="margin: 0;">-<span id="LC128" class="line" lang="plaintext"> <span class="idiff left right"> </span>one pattern source when running single threaded.</span>
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129
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<pre style="margin: 0;">-<span id="LC129" class="line" lang="plaintext"><span class="idiff left right"> </span> * Fixed an issue causing `bowtie2` and `bowtie2-inspect` to crash if</span>
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130
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<pre style="margin: 0;">-<span id="LC130" class="line" lang="plaintext"> <span class="idiff left right"> </span>the index contains a gap-only segment.</span>
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131
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<pre style="margin: 0;">-<span id="LC131" class="line" lang="plaintext"><span class="idiff left right"> </span> * Added experimental BAM input mode `-b`. Works only with unpaired</span>
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132
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<pre style="margin: 0;">-<span id="LC132" class="line" lang="plaintext"> <span class="idiff left right"> </span>input reads and BAM files that are sorted by read name (`samtools</span>
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133
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<pre style="margin: 0;">-<span id="LC133" class="line" lang="plaintext"> <span class="idiff left right"> </span>sort -n`). BAM input mode also supports the following options:</span>
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134
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<pre style="margin: 0;">-<span id="LC134" class="line" lang="plaintext"> <span class="idiff left right"> </span>o `--preserve-sam-tags`: Preserve any optional fields present in BAM record</span>
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135
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<pre style="margin: 0;">-<span id="LC135" class="line" lang="plaintext"> <span class="idiff left right"> </span>o `--align-paired-reads`: Paired-end mode for BAM files</span>
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136
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<pre style="margin: 0;">-<span id="LC136" class="line" lang="plaintext"><span class="idiff left right"> </span> * Added experimental cmake support</span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="plaintext"><span class="idiff left">## </span>Version 2.4.3 - May 13, 2021<span class="idiff right"> ##</span></span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="plaintext"></span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="plaintext"> * Replaced TBB concurrency with C++ threads</span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="plaintext"> * Added native support for processing Zstd-compressed read files</span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="plaintext"> to bowtie2</span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="plaintext"> * Added native support for processing Zstd-compressed</span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="plaintext"> reference-genome files to bowtie2-build</span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="plaintext"> * Fixed an issue causing `bowtie2` to report incorrect alignments</span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="plaintext"> on big-endian machines</span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="plaintext"> * Fixed an issue causing `bowtie2` to incorrectly process BAM</span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="plaintext"> files on big-endian machines</span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="plaintext"> * Fixed an issue causing Bowtie2 to set an incorrect MAPQ when AS and</span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="plaintext"> XS are the maximum for read length</span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="plaintext"> * Add support for building on Apple M1 processors</span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="plaintext"></span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="plaintext"><span class="idiff left">## </span>Version 2.4.2 - Oct 5, 2020<span class="idiff right"> ##</span></span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="plaintext"></span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="plaintext"> * Fixed an issue that would cause the `bowtie2` wrapper script to throw</span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="plaintext"> an error when using wrapper-specific arguments.</span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="plaintext"> * Added new `--sam-append-comment` flag that appends comment from FASTA/Q</span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="plaintext"> read to corresponding SAM record.</span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="plaintext"> * Fixed an issue that would cause qupto, `-u`, to overflow when there</span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="plaintext"> are >= 2^32 query sequences (PR #312).</span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="plaintext"> * Fixed an issue that would cause bowtie2-build script to incorrectly</span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="plaintext"> process reference files.</span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="plaintext"></span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="plaintext"><span class="idiff left">## </span>Version 2.4.1 - Feb 28, 2020<span class="idiff right"> ##</span></span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="plaintext"></span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="plaintext"> * Fixed an issue that would cause the `bowtie2` wrapper script to incorrectly</span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="plaintext"> process certain arguments.</span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="plaintext"></span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="plaintext"><span class="idiff left">## </span>Version 2.4.0 - Feb 25, 2020<span class="idiff right"> ##</span></span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="plaintext"></span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="plaintext"> * Fixed an issue in `-b <bam>` input mode where one might prematurely close the</span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="plaintext"> read file pointer causing "Bad file descriptor" in other threads</span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="plaintext"> * Fixed an issue that could cause `bowtie2` to crash in `--no-1mm-upfront` mode</span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="plaintext"> * Modified `bowtie2-build` to better handle of flags and positional parameters</span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="plaintext"> * Migrated all `python` scripts to `python3`</span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="plaintext"> * Added support for wildcards in input files to `bowtie2`, e.g. `bowtie2 -x</span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="plaintext"> index -q *.fq` as opposed to `bowtie2 -x index -q 1.fq,2.fq,3.fq...`</span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="plaintext"> * Fixed an issue causing <code>bowtie2</code> to incorrectly process read names</span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="plaintext"> with slash mates plus extra characters (see</span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="plaintext"> [#265](https://github.com/BenLangmead/bowtie2/issues/265))</span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="plaintext"> * Clarified support for overriding presets with more specific options e.g</span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="plaintext"> `bowtie2 -x index --local --very-fast-local --L22 -q reads.fq` will set the</span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="plaintext"> seed length to 22, overriding the 25 set by `--very-fast-local`</span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="plaintext"> * Modified SAM output for `-k`/`-a` so that supplementary alignments get</span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="plaintext"> assigned a MAPQ of 255</span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="plaintext"> * Fixed an issue that would sometimes cause `bowtie2-build` to not generate</span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="plaintext"> reverse index files</span>
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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="plaintext"> * Added preliminary support for ppc64le architectures with the help of SIMDE</span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="plaintext"> project (see [#271](https://github.com/BenLangmead/bowtie2/issues/271))</span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="plaintext"> * Fixed an issue causing `bowtie2` to incorrectly calculate the MAPQ when `--mp`</span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="plaintext"> was specified in combination with `--ignore-quals`</span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="plaintext"></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">## </span>Version 2.3.5.1 - Apr 16, 2019<span class="idiff right"> ##</span></span>
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="plaintext"></span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="plaintext"> * Added official support for BAM input files</span>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="plaintext"> * Added official support for CMake build system</span>
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124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="plaintext"> * Added changes to Makefile for creating Reproducible builds (via [210](https://github.com/BenLangmead/bowtie2/pull/210))</span>
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="plaintext"> * Fix an issue whereby building on aarch64 would require patching sed commands (via [#243](https://github.com/BenLangmead/bowtie2/pull/243))</span>
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126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="plaintext"> * Fix an issue whereby `bowtie2` would incorrectly throw an error while processing `--interleaved` input</span>
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127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="plaintext"><span class="idiff left">## </span>Version 2.3.5 - Mar 16, 2019<span class="idiff right"> ##</span></span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="plaintext"> * Added support for obtaining input reads directly from the Sequence Read Archive, via NCBI's [NGS language bindings](https://github.com/ncbi/ngs). This is activated via the [`--sra-acc`](manual.shtml#bowtie2-options-sra-acc) option. This implementation is based on Daehwan Kim's in [HISAT2](https://ccb.jhu.edu/software/hisat2). Supports both unpaired and paired-end inputs.</span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="plaintext"> * Bowtie 2 now compiles on ARM architectures (via [#216](https://github.com/BenLangmead/bowtie2/pull/216))</span>
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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="plaintext"> * `--interleaved` can now be combined with FASTA inputs (worked only with FASTQ before)</span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="plaintext"> * Fixed issue whereby large indexes were not successfully found in the `$BOWTIE2_INDEXES` directory</span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="plaintext"> * Fixed input from FIFOs (e.g. via process substitution) to distinguish gzip-compressed versus uncompressed input</span>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="plaintext"> * Fixed issue whereby arguments containing `bz2` `lz4` were misinterpretted as files</span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="plaintext"> * Fixed several compiler warnings</span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="plaintext"> * Fixed issue whereby both ends of a paired-end read could have negative TLEN if they exactly coincided</span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="plaintext"> * Fixed issue whereby `bowtie2-build` would hang on end-of-file (via [#228](https://github.com/BenLangmead/bowtie2/pull/228))</span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="plaintext"> * Fixed issue whereby wrapper script would sometimes create zombie processes (via [#51](https://github.com/BenLangmead/bowtie2/pull/51))</span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="plaintext"> * Fixed issue whereby `bowtie2-build` and `bowtie2-inspect` wrappers would fail on some versions of Python/PyPy</span>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="plaintext"> * Replaced old, unhelpful `README.md` in the project with a version that includes badges, links and some highlights from the manual</span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="plaintext"> * Note: BAM input support and CMake build support both remain experimental, but we expect to finalize them in the next release</span>
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143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="plaintext"><span class="idiff left">## </span>Version 2.3.4.3 - Sep 17, 2018<span class="idiff right"> ##</span></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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<pre style="margin: 0;">+<span id="LC146" class="line" lang="plaintext"> * Fixed an issue causing `bowtie2-build` and `bowtie2-inspect`</span>
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147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="plaintext"> to output incomplete help text.</span>
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148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="plaintext"> * Fixed an issue causing `bowtie2-inspect` to crash.</span>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="plaintext"> * Fixed an issue preventing `bowtie2` from processing paired and/or</span>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="plaintext"> unpaired FASTQ reads together with interleaved FASTQ reads.</span>
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151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="plaintext"><span class="idiff left">## </span>Version 2.3.4.2 - Aug 7, 2018<span class="idiff right"> ##</span></span>
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153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="plaintext"></span>
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154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="plaintext"> * Fixed issue causing `bowtie2` to fail in `--fast-local` mode.</span>
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="plaintext"> * Fixed issue causing `--soft-clipped-unmapped-tlen` to be a positional argument.</span>
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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="plaintext"> * New option `--trim-to N` causes `bowtie2` to trim reads longer</span>
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157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="plaintext"> than `N` bases to exactly `N` bases. Can trim from either 3'</span>
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158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="plaintext"> or 5' end, e.g. `--trim-to 5:30` trims reads to 30 bases,</span>
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159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="plaintext"> truncating at the 5' end.</span>
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160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="plaintext"> * Updated "Building from source" manual section with additional</span>
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161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="plaintext"> instructions on installing TBB.</span>
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162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="plaintext"> * Several other updates to manual, including new mentions of</span>
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163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="plaintext"> [Bioconda](http://bioconda.github.io) and</span>
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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="plaintext"> [Biocontainers](https://biocontainers.pro).</span>
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165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="plaintext"> * Fixed an issue preventing `bowtie2` from processing more than</span>
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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="plaintext"> one pattern source when running single threaded.</span>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="plaintext"> * Fixed an issue causing `bowtie2` and `bowtie2-inspect` to crash if</span>
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168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="plaintext"> the index contains a gap-only segment.</span>
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="plaintext"> * Added experimental BAM input mode `-b`. Works only with unpaired</span>
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170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="plaintext"> input reads and BAM files that are sorted by read name (`samtools</span>
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171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="plaintext"> sort -n`). BAM input mode also supports the following options:</span>
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172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="plaintext"> o `--preserve-sam-tags`: Preserve any optional fields present in BAM record</span>
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173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="plaintext"> o `--align-paired-reads`: Paired-end mode for BAM files</span>
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174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="plaintext"> * Added experimental cmake support</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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138
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176
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<pre style="margin: 0;"> <span id="LC176" class="line" lang="plaintext">Thread-scaling paper appears - July 19, 2018</span>
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139
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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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140
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<pre style="margin: 0;">-<span id="LC140" class="line" lang="plaintext"><span class="idiff left right"> </span> * Our latest work on Bowtie's core thread scaling capabilities</span>
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<pre style="margin: 0;">-<span id="LC141" class="line" lang="plaintext"> <span class="idiff left right"> </span>[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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178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="plaintext"> * Our latest work on Bowtie's core thread scaling capabilities</span>
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179
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<pre style="margin: 0;">+<span id="LC179" 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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142
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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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143
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<pre style="margin: 0;">-<span id="LC143" class="line" lang="plaintext">Version 2.3.4.1 - Feb 3, 2018</span>
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181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="plaintext"><span class="idiff left">## </span>Version 2.3.4.1 - Feb 3, 2018<span class="idiff right"> ##</span></span>
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144
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182
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<pre style="margin: 0;"> <span id="LC182" class="line" lang="plaintext"></span>
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145
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<pre style="margin: 0;">-<span id="LC145" class="line" lang="plaintext"><span class="idiff left right"> </span> * Fixed an issue with `--reorder` that caused bowtie2 to crash</span>
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146
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<pre style="margin: 0;">-<span id="LC146" class="line" lang="plaintext"> <span class="idiff left right"> </span>while reordering SAM output</span>
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183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="plaintext"> * Fixed an issue with `--reorder` that caused bowtie2 to crash</span>
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184
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="plaintext"> while reordering SAM output</span>
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147
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185
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<pre style="margin: 0;"> <span id="LC185" class="line" lang="plaintext"></span>
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148
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<pre style="margin: 0;">-<span id="LC148" class="line" lang="plaintext">Version 2.3.4 - Dec 29, 2017</span>
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186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="plaintext"><span class="idiff left">## </span>Version 2.3.4 - Dec 29, 2017<span class="idiff right"> ##</span></span>
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149
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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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150
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<pre style="margin: 0;">-<span id="LC150" class="line" lang="plaintext"><span class="idiff left right"> </span> * Fixed major issue causing corrupt SAM output when using many</span>
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151
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<pre style="margin: 0;">-<span id="LC151" class="line" lang="plaintext"> <span class="idiff left right"> </span>threads (-p/--threads) on certain systems.</span>
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152
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<pre style="margin: 0;">-<span id="LC152" class="line" lang="plaintext"><span class="idiff left right"> </span> * Fixed an issue whereby bowtie2 processes could overwrite each</span>
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153
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<pre style="margin: 0;">-<span id="LC153" class="line" lang="plaintext"> <span class="idiff left right"> </span>others' named pipes on HPC systems.</span>
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154
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<pre style="margin: 0;">-<span id="LC154" class="line" lang="plaintext"><span class="idiff left right"> </span> * Fixed an issue causing bowtie2-build and bowtie2-inspect to</span>
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155
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<pre style="margin: 0;">-<span id="LC155" class="line" lang="plaintext"> <span class="idiff left right"> </span>return prematurely on Windows.</span>
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156
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<pre style="margin: 0;">-<span id="LC156" class="line" lang="plaintext"><span class="idiff left right"> </span> * Fixed issues raised by compiler "sanitizers" that could</span>
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157
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<pre style="margin: 0;">-<span id="LC157" class="line" lang="plaintext"> <span class="idiff left right"> </span>potentially have caused memory corruption or undefined behavior.</span>
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158
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<pre style="margin: 0;">-<span id="LC158" class="line" lang="plaintext"><span class="idiff left right"> </span> * Added the "continuous FASTA" input format (`-F`) for aligning</span>
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159
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<pre style="margin: 0;">-<span id="LC159" class="line" lang="plaintext"> <span class="idiff left right"> </span>all the k-mers in the sequences of a FASTA file. Useful for</span>
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160
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<pre style="margin: 0;">-<span id="LC160" class="line" lang="plaintext"> <span class="idiff left right"> </span>determining mapability of regions of the genome, and similar</span>
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161
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<pre style="margin: 0;">-<span id="LC161" class="line" lang="plaintext"> <span class="idiff left right"> </span>tasks.</span>
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188
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="plaintext"> * Fixed major issue causing corrupt SAM output when using many</span>
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189
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="plaintext"> threads (-p/--threads) on certain systems.</span>
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190
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="plaintext"> * Fixed an issue whereby bowtie2 processes could overwrite each</span>
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191
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="plaintext"> others' named pipes on HPC systems.</span>
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192
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="plaintext"> * Fixed an issue causing bowtie2-build and bowtie2-inspect to</span>
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193
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="plaintext"> return prematurely on Windows.</span>
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194
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="plaintext"> * Fixed issues raised by compiler "sanitizers" that could</span>
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195
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="plaintext"> potentially have caused memory corruption or undefined behavior.</span>
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196
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="plaintext"> * Added the "continuous FASTA" input format (`-F`) for aligning</span>
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197
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="plaintext"> all the k-mers in the sequences of a FASTA file. Useful for</span>
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198
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="plaintext"> determining mapability of regions of the genome, and similar</span>
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199
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="plaintext"> tasks.</span>
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162
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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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163
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<pre style="margin: 0;">-<span id="LC163" class="line" lang="plaintext">Version 2.3.3.1 - Oct 05, 2017</span>
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201
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="plaintext"><span class="idiff left">## </span>Version 2.3.3.1 - Oct 05, 2017<span class="idiff right"> ##</span></span>
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164
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202
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<pre style="margin: 0;"> <span id="LC202" class="line" lang="plaintext"></span>
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165
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<pre style="margin: 0;">-<span id="LC165" class="line" lang="plaintext"> * Fixed an issue causing input files to be skipped when running</span>
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166
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<pre style="margin: 0;">-<span id="LC166" class="line" lang="plaintext"> multi-threaded alignment</span>
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167
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<pre style="margin: 0;">-<span id="LC167" class="line" lang="plaintext"> * Fixed an issue causing the first character of a read name to be</span>
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168
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<pre style="margin: 0;">-<span id="LC168" class="line" lang="plaintext"> dropped while parsing reads split across multiple input files</span>
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203
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="plaintext"> * Fixed an issue causing input files to be skipped when running</span>
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204
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="plaintext"> multi-threaded alignment</span>
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205
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="plaintext"> * Fixed an issue causing the first character of a read name to be</span>
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206
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="plaintext"> dropped while parsing reads split across multiple input files</span>
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207
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="plaintext"></span>
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208
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="plaintext">## Version 2.3.3 - Sep 09, 2017 ##</span>
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169
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209
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<pre style="margin: 0;"> <span id="LC209" class="line" lang="plaintext"></span>
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170
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<pre style="margin: 0;">-<span id="LC170" class="line" lang="plaintext">Version 2.3.3 - Sep 09, 2017</span>
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171
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210
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<pre style="margin: 0;"> <span id="LC210" class="line" lang="plaintext">From this release forward prepackaged bowtie2 binaries are now</span>
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172
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211
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<pre style="margin: 0;"> <span id="LC211" class="line" lang="plaintext">statically linked to the zlib compression library and, the recommended</span>
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173
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212
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<pre style="margin: 0;"> <span id="LC212" class="line" lang="plaintext">threading library, TBB. Users who rely on prepackaged builds are</span>
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174
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213
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<pre style="margin: 0;"> <span id="LC213" class="line" lang="plaintext">no longer required to have these packages pre-installed. As a result</span>
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175
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214
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<pre style="margin: 0;"> <span id="LC214" class="line" lang="plaintext">of the aforementioned changes legacy packages have been discontinued.</span>
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176
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215
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<pre style="margin: 0;"> <span id="LC215" class="line" lang="plaintext"></span>
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177
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<pre style="margin: 0;">-<span id="LC177" class="line" lang="plaintext"> * bowtie2-build now supports gzip-compressed FASTA inputs</span>
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178
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<pre style="margin: 0;">-<span id="LC178" class="line" lang="plaintext"> * New --xeq parameter for bowtie2 disambiguates the 'M' CIGAR</span>
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179
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<pre style="margin: 0;">-<span id="LC179" class="line" lang="plaintext"> flag. When specified, matches are indicated with the '=' operation and</span>
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180
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<pre style="margin: 0;">-<span id="LC180" class="line" lang="plaintext"> mismatches with 'X'</span>
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181
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<pre style="margin: 0;">-<span id="LC181" class="line" lang="plaintext"> * Fixed a possible infinite loop during parallel index building due</span>
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182
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<pre style="margin: 0;">-<span id="LC182" class="line" lang="plaintext"> to the compiler optimizing away a loop condition</span>
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183
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<pre style="margin: 0;">-<span id="LC183" class="line" lang="plaintext"> * Added --soft-clipped-unmapped-tlen parameter for bowtie2 that</span>
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<td class="old_line diff-line-num old" data-linenumber="184" 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">
184
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<pre style="margin: 0;">-<span id="LC184" class="line" lang="plaintext"> ignores soft-clipped bases when calculating template length (TLEN)</span>
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<td class="old_line diff-line-num old" data-linenumber="185" 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">
185
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<pre style="margin: 0;">-<span id="LC185" class="line" lang="plaintext"> * Added support for multi-line sequences in FASTA read inputs</span>
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<td class="old_line diff-line-num old" data-linenumber="186" 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">
186
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<pre style="margin: 0;">-<span id="LC186" class="line" lang="plaintext"> * Expanded explanation of MD:Z field in manual</span>
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<td class="old_line diff-line-num old" data-linenumber="187" 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">
187
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<pre style="margin: 0;">-<span id="LC187" class="line" lang="plaintext"> * Fixed a crashing bug when output is redirected to a pipe</span>
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<td class="old_line diff-line-num old" data-linenumber="188" 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">
188
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<pre style="margin: 0;">-<span id="LC188" class="line" lang="plaintext"> * Fixed ambiguity in the SEED alignment policy that sometimes caused -N parameter to be ignored</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">Version 2.3.2 - May 05, 2017</span>
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191
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<pre style="margin: 0;">-<span id="LC191" class="line" lang="plaintext"> * Added support for interleaved paired-end FASTQ inputs</span>
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192
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<pre style="margin: 0;">-<span id="LC192" class="line" lang="plaintext"> (--interleaved)</span>
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193
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<pre style="margin: 0;">-<span id="LC193" class="line" lang="plaintext"> * Now reports MREVERSE SAM flag for unaligned end when only one</span>
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194
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<pre style="margin: 0;">-<span id="LC194" class="line" lang="plaintext"> end of a pair aligns</span>
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195
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<pre style="margin: 0;">-<span id="LC195" class="line" lang="plaintext"> * Fixed issue where first character of some read names was</span>
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196
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<pre style="margin: 0;">-<span id="LC196" class="line" lang="plaintext"> omitted from SAM output when using tabbed input formats</span>
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197
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<pre style="margin: 0;">-<span id="LC197" class="line" lang="plaintext"> * Added --sam-no-qname-trunc option, which causes entire read</span>
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198
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<pre style="margin: 0;">-<span id="LC198" class="line" lang="plaintext"> name, including spaces, to be written to SAM output. This</span>
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199
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<pre style="margin: 0;">-<span id="LC199" class="line" lang="plaintext"> violates SAM specification, but can be useful in applications</span>
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200
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<pre style="margin: 0;">-<span id="LC200" class="line" lang="plaintext"> that immediately postprocess the SAM.</span>
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201
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<pre style="margin: 0;">-<span id="LC201" class="line" lang="plaintext"> * Fixed compilation error caused by pointer comparison issue</span>
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202
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<pre style="margin: 0;">-<span id="LC202" class="line" lang="plaintext"> in aligner_result.cpp</span>
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203
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<pre style="margin: 0;">-<span id="LC203" class="line" lang="plaintext"> * Removed termcap and readline dependencies introduced in v2.3.1</span>
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204
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<pre style="margin: 0;">-<span id="LC204" class="line" lang="plaintext"> * Fixed compilation issues caused by gzbuffer function when</span>
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205
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<pre style="margin: 0;">-<span id="LC205" class="line" lang="plaintext"> compiling with zlib v1.2.3.5 and earlier. Users compiling against</span>
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206
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<pre style="margin: 0;">-<span id="LC206" class="line" lang="plaintext"> these libraries will use the zlib default buffer size of 8Kb</span>
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207
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<pre style="margin: 0;">-<span id="LC207" class="line" lang="plaintext"> when decompressing read files.</span>
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208
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<pre style="margin: 0;">-<span id="LC208" class="line" lang="plaintext"> * Fixed issue that would cause Bowtie 2 hang when aligning FASTA</span>
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<td class="old_line diff-line-num old" data-linenumber="209" 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">
209
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<pre style="margin: 0;">-<span id="LC209" class="line" lang="plaintext"> inputs with more than one thread</span>
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210
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<pre style="margin: 0;">-<span id="LC210" class="line" lang="plaintext"></span>
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211
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<pre style="margin: 0;">-<span id="LC211" class="line" lang="plaintext">Version 2.3.1 - Mar 04, 2017</span>
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216
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="plaintext"> * bowtie2-build now supports gzip-compressed FASTA inputs</span>
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<td class="new_line diff-line-num new" data-linenumber="217" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
217
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="plaintext"> * New --xeq parameter for bowtie2 disambiguates the 'M' CIGAR</span>
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218
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="plaintext"> flag. When specified, matches are indicated with the '=' operation and</span>
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219
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="plaintext"> mismatches with 'X'</span>
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220
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="plaintext"> * Fixed a possible infinite loop during parallel index building due</span>
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221
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="plaintext"> to the compiler optimizing away a loop condition</span>
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222
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="plaintext"> * Added --soft-clipped-unmapped-tlen parameter for bowtie2 that</span>
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223
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="plaintext"> ignores soft-clipped bases when calculating template length (TLEN)</span>
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224
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="plaintext"> * Added support for multi-line sequences in FASTA read inputs</span>
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225
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="plaintext"> * Expanded explanation of MD:Z field in manual</span>
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226
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="plaintext"> * Fixed a crashing bug when output is redirected to a pipe</span>
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227
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<pre style="margin: 0;">+<span id="LC227" class="line" lang="plaintext"> * Fixed ambiguity in the SEED alignment policy that sometimes caused -N parameter to be ignored</span>
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228
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="plaintext"></span>
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229
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="plaintext">## Version 2.3.2 - May 05, 2017 ##</span>
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230
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<pre style="margin: 0;">+<span id="LC230" class="line" lang="plaintext"></span>
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231
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<pre style="margin: 0;">+<span id="LC231" class="line" lang="plaintext"> * Added support for interleaved paired-end FASTQ inputs</span>
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232
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<pre style="margin: 0;">+<span id="LC232" class="line" lang="plaintext"> (--interleaved)</span>
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233
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<pre style="margin: 0;">+<span id="LC233" class="line" lang="plaintext"> * Now reports MREVERSE SAM flag for unaligned end when only one</span>
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234
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<pre style="margin: 0;">+<span id="LC234" class="line" lang="plaintext"> end of a pair aligns</span>
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235
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="plaintext"> * Fixed issue where first character of some read names was</span>
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236
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<pre style="margin: 0;">+<span id="LC236" class="line" lang="plaintext"> omitted from SAM output when using tabbed input formats</span>
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237
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="plaintext"> * Added --sam-no-qname-trunc option, which causes entire read</span>
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238
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="plaintext"> name, including spaces, to be written to SAM output. This</span>
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239
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<pre style="margin: 0;">+<span id="LC239" class="line" lang="plaintext"> violates SAM specification, but can be useful in applications</span>
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240
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<pre style="margin: 0;">+<span id="LC240" class="line" lang="plaintext"> that immediately postprocess the SAM.</span>
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241
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<pre style="margin: 0;">+<span id="LC241" class="line" lang="plaintext"> * Fixed compilation error caused by pointer comparison issue</span>
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<pre style="margin: 0;">+<span id="LC242" class="line" lang="plaintext"> in aligner_result.cpp</span>
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<pre style="margin: 0;">+<span id="LC243" class="line" lang="plaintext"> * Removed termcap and readline dependencies introduced in v2.3.1</span>
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<pre style="margin: 0;">+<span id="LC244" class="line" lang="plaintext"> * Fixed compilation issues caused by gzbuffer function when</span>
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<pre style="margin: 0;">+<span id="LC245" class="line" lang="plaintext"> compiling with zlib v1.2.3.5 and earlier. Users compiling against</span>
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<pre style="margin: 0;">+<span id="LC246" class="line" lang="plaintext"> these libraries will use the zlib default buffer size of 8Kb</span>
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="plaintext"> when decompressing read files.</span>
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<pre style="margin: 0;">+<span id="LC248" class="line" lang="plaintext"> * Fixed issue that would cause Bowtie 2 hang when aligning FASTA</span>
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<pre style="margin: 0;">+<span id="LC249" class="line" lang="plaintext"> inputs with more than one thread</span>
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<pre style="margin: 0;">+<span id="LC250" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC251" class="line" lang="plaintext">## Version 2.3.1 - Mar 04, 2017 ##</span>
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<pre style="margin: 0;">+<span id="LC252" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC253" class="line" lang="plaintext">Please note that as of this release Bowtie 2 now has dependencies on zlib and readline libraries.</span>
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<pre style="margin: 0;"> <span id="LC254" class="line" lang="plaintext">Make sure that all dependencies are met before attempting to build from source.</span>
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<pre style="margin: 0;"> <span id="LC255" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC215" class="line" lang="plaintext"> * Added native support for gzipped read files. The wrapper</span>
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<pre style="margin: 0;">-<span id="LC216" class="line" lang="plaintext"> script is no longer responsible for decompression. This</span>
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<pre style="margin: 0;">-<span id="LC217" class="line" lang="plaintext"> simplifies the wrapper and improves speed and thread scalability</span>
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<pre style="margin: 0;">-<span id="LC218" class="line" lang="plaintext"> for gzipped inputs.</span>
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<pre style="margin: 0;">-<span id="LC219" class="line" lang="plaintext"> * Fixed a bug that caused `bowtie2-build` to crash when the</span>
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<pre style="margin: 0;">-<span id="LC220" class="line" lang="plaintext"> first FASTA sequence contains all Ns.</span>
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221
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<pre style="margin: 0;">-<span id="LC221" class="line" lang="plaintext"> * Add support for interleaved FASTQ format (`--interleaved`)</span>
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<pre style="margin: 0;">-<span id="LC222" class="line" lang="plaintext"> * Empty FASTQ inputs would yield an error in Bowtie 2 2.3.0,</span>
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223
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<pre style="margin: 0;">-<span id="LC223" class="line" lang="plaintext"> whereas previous versions would simply align 0 reads and report</span>
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<pre style="margin: 0;">-<span id="LC224" class="line" lang="plaintext"> the SAM header as usual. This version returns to the pre-2.3.0</span>
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<pre style="margin: 0;">-<span id="LC225" class="line" lang="plaintext"> behavior, resolving a compatibility issue between TopHat2 and</span>
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<pre style="margin: 0;">-<span id="LC226" class="line" lang="plaintext"> Bowtie 2 2.3.0.</span>
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<pre style="margin: 0;">-<span id="LC227" class="line" lang="plaintext"> * Fixed a bug whereby combining `--un-conc*` with `-k` or `-a`</span>
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<pre style="margin: 0;">-<span id="LC228" class="line" lang="plaintext"> would cause `bowtie2` to print duplicate reads in one or both</span>
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229
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<pre style="margin: 0;">-<span id="LC229" class="line" lang="plaintext"> of the `--un-conc*` output files, causing the ends to be</span>
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<pre style="margin: 0;">-<span id="LC230" class="line" lang="plaintext"> misaligned.</span>
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<pre style="margin: 0;">-<span id="LC231" class="line" lang="plaintext"> * The default `--score-min` for `--local` mode is now `G,20,8`.</span>
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<pre style="margin: 0;">-<span id="LC232" class="line" lang="plaintext"> That was the stated default in the documentation for a while,</span>
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<pre style="margin: 0;">-<span id="LC233" class="line" lang="plaintext"> but the actual default was `G,0,10` for many versions. Now the</span>
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<pre style="margin: 0;">-<span id="LC234" class="line" lang="plaintext"> default matches the documentation and, we find, yields more</span>
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<pre style="margin: 0;">-<span id="LC235" class="line" lang="plaintext"> accurate alignments than `G,0,10`</span>
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<pre style="margin: 0;">-<span id="LC236" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC237" class="line" lang="plaintext">Version 2.3.0 - Dec 13, 2016</span>
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<pre style="margin: 0;">-<span id="LC238" class="line" lang="plaintext"> * Code related to read parsing was completely rewritten to improve</span>
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<pre style="margin: 0;">-<span id="LC239" class="line" lang="plaintext"> scalability to many threads. In short, the critical section is</span>
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<pre style="margin: 0;">-<span id="LC240" class="line" lang="plaintext"> simpler and parses input reads in batches rather than one at a time.</span>
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<pre style="margin: 0;">-<span id="LC241" class="line" lang="plaintext"> The improvement applies to all read formats.</span>
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<pre style="margin: 0;">-<span id="LC242" class="line" lang="plaintext"> * TBB is now the default threading library. We consistently found TBB to give</span>
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<pre style="margin: 0;">-<span id="LC243" class="line" lang="plaintext"> superior thread scaling. It is widely available and widely installed.</span>
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<pre style="margin: 0;">-<span id="LC244" class="line" lang="plaintext"> That said, we are also preserving a "legacy" version of Bowtie that,</span>
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<pre style="margin: 0;">-<span id="LC245" class="line" lang="plaintext"> like previous releases, does not use TBB. To compile Bowtie source</span>
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<pre style="margin: 0;">-<span id="LC246" class="line" lang="plaintext"> in legacy mode use `NO_TBB=1`. To</span>
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<pre style="margin: 0;">-<span id="LC247" class="line" lang="plaintext"> use legacy binaries, download the appropriate binary archive with</span>
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<pre style="margin: 0;">-<span id="LC248" class="line" lang="plaintext"> "legacy" in the name.</span>
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<pre style="margin: 0;">-<span id="LC249" class="line" lang="plaintext"> * Bowtie now uses a queue-based lock rather</span>
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250
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<pre style="margin: 0;">-<span id="LC250" class="line" lang="plaintext"> than a spin or heavyweight lock. We find this gives superior thread</span>
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<pre style="margin: 0;">-<span id="LC251" class="line" lang="plaintext"> scaling; we saw an order-of-magnitude throughput improvements at</span>
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<pre style="margin: 0;">-<span id="LC252" class="line" lang="plaintext"> 120 threads in one experiment, for example.</span>
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<pre style="margin: 0;">-<span id="LC253" class="line" lang="plaintext"> * Unnecessary thread synchronization removed</span>
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<pre style="margin: 0;">-<span id="LC254" class="line" lang="plaintext"> * Fixed issue with parsing FASTA records with greater-than symbol in the name</span>
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<pre style="margin: 0;">-<span id="LC255" class="line" lang="plaintext"> * Now detects and reports inconsistencies between `--score-min` and `--ma`</span>
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256
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<pre style="margin: 0;">-<span id="LC256" class="line" lang="plaintext"> * Changed default for `--bmaxdivn` to yield better memory footprint and running time when building an index with many threads</span>
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257
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<pre style="margin: 0;">-<span id="LC257" class="line" lang="plaintext"></span>
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258
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<pre style="margin: 0;">-<span id="LC258" class="line" lang="plaintext">Version 2.2.9 - Apr 22, 2016</span>
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259
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<pre style="margin: 0;">-<span id="LC259" class="line" lang="plaintext"> * Fixed the multiple threads issue for the bowtie2-build.</span>
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260
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<pre style="margin: 0;">-<span id="LC260" class="line" lang="plaintext"> * Fixed a TBB related build issue impacting TBB v4.4.</span>
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<td class="old_line diff-line-num old" data-linenumber="261" 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">
261
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<pre style="margin: 0;">-<span id="LC261" class="line" lang="plaintext"></span>
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<td class="old_line diff-line-num old" data-linenumber="262" 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">
262
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<pre style="margin: 0;">-<span id="LC262" class="line" lang="plaintext">Version 2.2.8 - Mar 10, 2016</span>
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263
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<pre style="margin: 0;">-<span id="LC263" class="line" lang="plaintext"> * Various website updates.</span>
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264
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<pre style="margin: 0;">-<span id="LC264" class="line" lang="plaintext"> * Fixed the bowtie2-build issue that made TBB compilation fail.</span>
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265
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<pre style="margin: 0;">-<span id="LC265" class="line" lang="plaintext"> * Fixed the static build for Win32 platform.</span>
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266
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<pre style="margin: 0;">-<span id="LC266" class="line" lang="plaintext"> </span>
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267
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<pre style="margin: 0;">-<span id="LC267" class="line" lang="plaintext"></span>
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268
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<pre style="margin: 0;">-<span id="LC268" class="line" lang="plaintext">Version 2.2.7 - Feb 10, 2016</span>
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<td class="old_line diff-line-num old" data-linenumber="269" 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">
269
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<pre style="margin: 0;">-<span id="LC269" class="line" lang="plaintext"> * Added a parallel index build option: bowtie2-build --threads <# threads>.</span>
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<td class="old_line diff-line-num old" data-linenumber="270" 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">
270
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<pre style="margin: 0;">-<span id="LC270" class="line" lang="plaintext"> * Fixed an issue whereby IUPAC codes (other than A/C/G/T/N) in reads were</span>
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<td class="old_line diff-line-num old" data-linenumber="271" 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">
271
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<pre style="margin: 0;">-<span id="LC271" class="line" lang="plaintext"> converted to As. Now all non-A/C/G/T characters in reads become Ns.</span>
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<td class="old_line diff-line-num old" data-linenumber="272" 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">
272
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<pre style="margin: 0;">-<span id="LC272" class="line" lang="plaintext"> * Fixed some compilation issues, including for the Intel C++ Compiler.</span>
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<td class="old_line diff-line-num old" data-linenumber="273" 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">
273
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<pre style="margin: 0;">-<span id="LC273" class="line" lang="plaintext"> * Removed debugging code that could impede performance for many alignment</span>
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274
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<pre style="margin: 0;">-<span id="LC274" class="line" lang="plaintext"> threads.</span>
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275
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<pre style="margin: 0;">-<span id="LC275" class="line" lang="plaintext"> * Fixed a few typos in documentation.</span>
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276
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<pre style="margin: 0;">-<span id="LC276" class="line" lang="plaintext"></span>
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<td class="old_line diff-line-num old" data-linenumber="277" 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">
277
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<pre style="margin: 0;">-<span id="LC277" class="line" lang="plaintext">Version 2.2.6 - Jul 22, 2015</span>
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<td class="old_line diff-line-num old" data-linenumber="278" 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">
278
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<pre style="margin: 0;">-<span id="LC278" class="line" lang="plaintext"> * Switched to a stable sort to avoid some potential reproducibility confusions.</span>
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<td class="old_line diff-line-num old" data-linenumber="279" 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">
279
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<pre style="margin: 0;">-<span id="LC279" class="line" lang="plaintext"> * Added 'install' target for *nix platforms.</span>
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<td class="old_line diff-line-num old" data-linenumber="280" 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">
280
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<pre style="margin: 0;">-<span id="LC280" class="line" lang="plaintext"> * Added the Intel TBB option which provides in most situations a better performance</span>
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<td class="old_line diff-line-num old" data-linenumber="281" 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">
281
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<pre style="margin: 0;">-<span id="LC281" class="line" lang="plaintext"> output. TBB is not present by default in the current build but can be added </span>
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282
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<pre style="margin: 0;">-<span id="LC282" class="line" lang="plaintext"> by compiling the source code with WITH_TBB=1 option.</span>
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<td class="old_line diff-line-num old" data-linenumber="283" 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">
283
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<pre style="margin: 0;">-<span id="LC283" class="line" lang="plaintext"> * Fixed a bug that caused seed lenght to be dependent of the -L and -N parameters order.</span>
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<td class="old_line diff-line-num old" data-linenumber="284" 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">
284
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<pre style="margin: 0;">-<span id="LC284" class="line" lang="plaintext"> * Fixed a bug that caused --local followed by -N to reset seed lenght to 22 which is</span>
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<td class="old_line diff-line-num old" data-linenumber="285" 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">
285
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<pre style="margin: 0;">-<span id="LC285" class="line" lang="plaintext"> actually the default value for global.</span>
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<td class="old_line diff-line-num old" data-linenumber="286" 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">
286
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<pre style="margin: 0;">-<span id="LC286" class="line" lang="plaintext"> * Enable compilation on FreeBSD and clang, although gmake port is still required.</span>
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<td class="old_line diff-line-num old" data-linenumber="287" 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">
287
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<pre style="margin: 0;">-<span id="LC287" class="line" lang="plaintext"> * Fixed an issue that made bowtie2 compilation process to fail on Snow Leopard.</span>
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288
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<pre style="margin: 0;">-<span id="LC288" class="line" lang="plaintext"></span>
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289
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<pre style="margin: 0;">-<span id="LC289" class="line" lang="plaintext"></span>
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290
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<pre style="margin: 0;">-<span id="LC290" class="line" lang="plaintext">Version 2.2.5 - Mar 9, 2015</span>
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<td class="old_line diff-line-num old" data-linenumber="291" 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">
291
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<pre style="margin: 0;">-<span id="LC291" class="line" lang="plaintext"> * Fixed some situations where incorrectly we could detect a Mavericks platform.</span>
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<td class="old_line diff-line-num old" data-linenumber="292" 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">
292
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<pre style="margin: 0;">-<span id="LC292" class="line" lang="plaintext"> * Fixed some manual issues including some HTML bad formating.</span>
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<td class="old_line diff-line-num old" data-linenumber="293" 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">
293
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<pre style="margin: 0;">-<span id="LC293" class="line" lang="plaintext"> * Make sure the wrapper correctly identifies the platform under OSX.</span>
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<td class="old_line diff-line-num old" data-linenumber="294" 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">
294
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<pre style="margin: 0;">-<span id="LC294" class="line" lang="plaintext"> * Fixed --rg/--rg-id options where included spaces were incorrectly treated.</span>
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<td class="old_line diff-line-num old" data-linenumber="295" 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">
295
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<pre style="margin: 0;">-<span id="LC295" class="line" lang="plaintext"> * Various documentation fixes added by contributors.</span>
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<td class="old_line diff-line-num old" data-linenumber="296" 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">
296
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<pre style="margin: 0;">-<span id="LC296" class="line" lang="plaintext"> * Fixed the incorrect behavior where parameter file names may contain spaces.</span>
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<td class="old_line diff-line-num old" data-linenumber="297" 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">
297
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<pre style="margin: 0;">-<span id="LC297" class="line" lang="plaintext"> * Fixed bugs related with the presence of spaces in the path where bowtie binaries are stored.</span>
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<td class="old_line diff-line-num old" data-linenumber="298" 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">
298
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<pre style="margin: 0;">-<span id="LC298" class="line" lang="plaintext"> * Improved exception handling for missformated quality values. </span>
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<td class="old_line diff-line-num old" data-linenumber="299" 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">
299
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<pre style="margin: 0;">-<span id="LC299" class="line" lang="plaintext"> * Improved redundancy checks by correctly account for soft clipping. </span>
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300
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<pre style="margin: 0;">-<span id="LC300" class="line" lang="plaintext"></span>
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<td class="old_line diff-line-num old" data-linenumber="301" 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">
301
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<pre style="margin: 0;">-<span id="LC301" class="line" lang="plaintext">Version 2.2.4 - Oct 22, 2014</span>
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<td class="old_line diff-line-num old" data-linenumber="302" 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">
302
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<pre style="margin: 0;">-<span id="LC302" class="line" lang="plaintext"> * Fixed a Mavericks OSX specific bug caused by some linkage ambiguities.</span>
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<td class="old_line diff-line-num old" data-linenumber="303" 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">
303
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<pre style="margin: 0;">-<span id="LC303" class="line" lang="plaintext"> * Added lz4 compression option for the wrapper.</span>
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<td class="old_line diff-line-num old" data-linenumber="304" 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">
304
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<pre style="margin: 0;">-<span id="LC304" class="line" lang="plaintext"> * Fixed the vanishing --no-unal help line.</span>
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<td class="old_line diff-line-num old" data-linenumber="305" 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">
305
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<pre style="margin: 0;">-<span id="LC305" class="line" lang="plaintext"> * Added the static linkage for MinGW builds.</span>
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<td class="old_line diff-line-num old" data-linenumber="306" 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">
306
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<td class="new_line diff-line-num old" data-linenumber="256" 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="LC306" class="line" lang="plaintext"> * Added extra seed-hit output.</span>
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307
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<pre style="margin: 0;">-<span id="LC307" class="line" lang="plaintext"> * Fixed missing 0-length read in fastq --passthrough output.</span>
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308
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<pre style="margin: 0;">-<span id="LC308" class="line" lang="plaintext"> * Fixed an issue that would cause different output in -a mode depending on random seed.</span>
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309
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<pre style="margin: 0;">-<span id="LC309" class="line" lang="plaintext"></span>
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310
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<pre style="margin: 0;">-<span id="LC310" class="line" lang="plaintext">Version 2.2.3 - May 30, 2014</span>
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311
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<pre style="margin: 0;">-<span id="LC311" class="line" lang="plaintext"> * Fixed a bug that made loading an index into memory crash sometimes.</span>
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<td class="old_line diff-line-num old" data-linenumber="312" 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">
312
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<pre style="margin: 0;">-<span id="LC312" class="line" lang="plaintext"> * Fixed a silent failure to warn the user in case the -x option is missing.</span>
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<td class="old_line diff-line-num old" data-linenumber="313" 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">
313
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<pre style="margin: 0;">-<span id="LC313" class="line" lang="plaintext"> * Updated al, un, al-conc and un-conc options to avoid confusion in cases</span>
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314
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<pre style="margin: 0;">-<span id="LC314" class="line" lang="plaintext"> where the user does not provide a base file name.</span>
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<td class="old_line diff-line-num old" data-linenumber="315" 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">
315
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<pre style="margin: 0;">-<span id="LC315" class="line" lang="plaintext"> * Fixed a spurious assert that made bowtie2-inspect debug fail. </span>
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316
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<pre style="margin: 0;">-<span id="LC316" class="line" lang="plaintext"></span>
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317
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<pre style="margin: 0;">-<span id="LC317" class="line" lang="plaintext">Version 2.2.2 - April 10, 2014</span>
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318
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<pre style="margin: 0;">-<span id="LC318" class="line" lang="plaintext"> * Improved performance for cases where the reference contains ambiguous </span>
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319
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<pre style="margin: 0;">-<span id="LC319" class="line" lang="plaintext"> or masked nucleobases represented by Ns. </span>
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320
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<pre style="margin: 0;">-<span id="LC320" class="line" lang="plaintext"></span>
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321
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<pre style="margin: 0;">-<span id="LC321" class="line" lang="plaintext">Version 2.2.1 - February 28, 2014</span>
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322
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<pre style="margin: 0;">-<span id="LC322" class="line" lang="plaintext"> * Improved way in which index files are loaded for alignment. Should fix</span>
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323
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<pre style="margin: 0;">-<span id="LC323" class="line" lang="plaintext"> efficiency problems on some filesystems.</span>
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324
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<pre style="margin: 0;">-<span id="LC324" class="line" lang="plaintext"> * Fixed a bug that made older systems unable to correctly deal with bowtie </span>
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325
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<pre style="margin: 0;">-<span id="LC325" class="line" lang="plaintext"> relative symbolic links.</span>
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326
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<pre style="margin: 0;">-<span id="LC326" class="line" lang="plaintext"> * Fixed a bug that, for very big indexes, could determine to determine file</span>
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327
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<pre style="margin: 0;">-<span id="LC327" class="line" lang="plaintext"> offsets correctly.</span>
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328
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<pre style="margin: 0;">-<span id="LC328" class="line" lang="plaintext"> * Fixed a bug where using --no-unal option incorrectly suppressed</span>
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329
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<pre style="margin: 0;">-<span id="LC329" class="line" lang="plaintext"> --un/--un-conc output.</span>
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330
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<pre style="margin: 0;">-<span id="LC330" class="line" lang="plaintext"> * Dropped a perl dependency that could cause problems on old systems.</span>
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331
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<pre style="margin: 0;">-<span id="LC331" class="line" lang="plaintext"> * Added --no-1mm-upfront option and clarified documentation for parameters</span>
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332
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<pre style="margin: 0;">-<span id="LC332" class="line" lang="plaintext"> governing the multiseed heuristic.</span>
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333
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<pre style="margin: 0;">-<span id="LC333" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC334" class="line" lang="plaintext">Version 2.2.0 - February 10, 2014</span>
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<pre style="margin: 0;">-<span id="LC335" class="line" lang="plaintext"> * Improved index querying efficiency using "population count" instructions</span>
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<pre style="margin: 0;">-<span id="LC336" class="line" lang="plaintext"> available since SSE4.2.</span>
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337
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<pre style="margin: 0;">-<span id="LC337" class="line" lang="plaintext"> * Added support for large and small indexes, removing 4-billion-nucleotide</span>
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338
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<pre style="margin: 0;">-<span id="LC338" class="line" lang="plaintext"> barrier. Bowtie 2 can now be used with reference genomes of any size.</span>
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339
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<pre style="margin: 0;">-<span id="LC339" class="line" lang="plaintext"> * Fixed bug that could cause bowtie2-build to crash when reference length</span>
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340
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<pre style="margin: 0;">-<span id="LC340" class="line" lang="plaintext"> is close to 4 billion.</span>
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341
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<pre style="margin: 0;">-<span id="LC341" class="line" lang="plaintext"> * Fixed issue in bowtie2-inspect that caused -e mode not to output</span>
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342
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<pre style="margin: 0;">-<span id="LC342" class="line" lang="plaintext"> nucleotides properly.</span>
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343
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<pre style="margin: 0;">-<span id="LC343" class="line" lang="plaintext"> * Added a CL: string to the @PG SAM header to preserve information about</span>
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344
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<pre style="margin: 0;">-<span id="LC344" class="line" lang="plaintext"> the aligner binary and paramteres.</span>
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345
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<pre style="margin: 0;">-<span id="LC345" class="line" lang="plaintext"> * No longer releasing 32-bit binaries. Simplified manual and Makefile</span>
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346
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<pre style="margin: 0;">-<span id="LC346" class="line" lang="plaintext"> accordingly.</span>
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347
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<pre style="margin: 0;">-<span id="LC347" class="line" lang="plaintext"> * Credits to the Intel(r) enabling team for performance optimizations</span>
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348
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<pre style="margin: 0;">-<span id="LC348" class="line" lang="plaintext"> included in this release. Thank you!</span>
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349
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<pre style="margin: 0;">-<span id="LC349" class="line" lang="plaintext"> * Phased out CygWin support.</span>
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350
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<pre style="margin: 0;">-<span id="LC350" class="line" lang="plaintext"> * Added the .bat generation for Windows.</span>
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351
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<pre style="margin: 0;">-<span id="LC351" class="line" lang="plaintext"> * Fixed some issues with some uncommon chars in fasta files.</span>
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352
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<pre style="margin: 0;">-<span id="LC352" class="line" lang="plaintext"> * Fixed wrappers so bowtie can now be used with symlinks.</span>
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256
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<pre style="margin: 0;">+<span id="LC256" class="line" lang="plaintext"> * Added native support for gzipped read files. The wrapper</span>
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257
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<pre style="margin: 0;">+<span id="LC257" class="line" lang="plaintext"> script is no longer responsible for decompression. This</span>
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258
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<pre style="margin: 0;">+<span id="LC258" class="line" lang="plaintext"> simplifies the wrapper and improves speed and thread scalability</span>
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259
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<pre style="margin: 0;">+<span id="LC259" class="line" lang="plaintext"> for gzipped inputs.</span>
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260
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<pre style="margin: 0;">+<span id="LC260" class="line" lang="plaintext"> * Fixed a bug that caused `bowtie2-build` to crash when the</span>
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<td class="new_line diff-line-num new" data-linenumber="261" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
261
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<pre style="margin: 0;">+<span id="LC261" class="line" lang="plaintext"> first FASTA sequence contains all Ns.</span>
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262
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<pre style="margin: 0;">+<span id="LC262" class="line" lang="plaintext"> * Add support for interleaved FASTQ format (`--interleaved`)</span>
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263
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<pre style="margin: 0;">+<span id="LC263" class="line" lang="plaintext"> * Empty FASTQ inputs would yield an error in Bowtie 2 2.3.0,</span>
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264
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<pre style="margin: 0;">+<span id="LC264" class="line" lang="plaintext"> whereas previous versions would simply align 0 reads and report</span>
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265
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<pre style="margin: 0;">+<span id="LC265" class="line" lang="plaintext"> the SAM header as usual. This version returns to the pre-2.3.0</span>
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266
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<pre style="margin: 0;">+<span id="LC266" class="line" lang="plaintext"> behavior, resolving a compatibility issue between TopHat2 and</span>
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267
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<pre style="margin: 0;">+<span id="LC267" class="line" lang="plaintext"> Bowtie 2 2.3.0.</span>
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268
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<pre style="margin: 0;">+<span id="LC268" class="line" lang="plaintext"> * Fixed a bug whereby combining `--un-conc*` with `-k` or `-a`</span>
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269
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<pre style="margin: 0;">+<span id="LC269" class="line" lang="plaintext"> would cause `bowtie2` to print duplicate reads in one or both</span>
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270
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<pre style="margin: 0;">+<span id="LC270" class="line" lang="plaintext"> of the `--un-conc*` output files, causing the ends to be</span>
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271
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<pre style="margin: 0;">+<span id="LC271" class="line" lang="plaintext"> misaligned.</span>
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272
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<pre style="margin: 0;">+<span id="LC272" class="line" lang="plaintext"> * The default `--score-min` for `--local` mode is now `G,20,8`.</span>
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273
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<pre style="margin: 0;">+<span id="LC273" class="line" lang="plaintext"> That was the stated default in the documentation for a while,</span>
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274
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<pre style="margin: 0;">+<span id="LC274" class="line" lang="plaintext"> but the actual default was `G,0,10` for many versions. Now the</span>
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275
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<pre style="margin: 0;">+<span id="LC275" class="line" lang="plaintext"> default matches the documentation and, we find, yields more</span>
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276
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<pre style="margin: 0;">+<span id="LC276" class="line" lang="plaintext"> accurate alignments than `G,0,10`</span>
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277
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<pre style="margin: 0;">+<span id="LC277" class="line" lang="plaintext"></span>
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278
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<pre style="margin: 0;">+<span id="LC278" class="line" lang="plaintext">## Version 2.3.0 - Dec 13, 2016 ##</span>
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279
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<pre style="margin: 0;">+<span id="LC279" class="line" lang="plaintext"></span>
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280
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<pre style="margin: 0;">+<span id="LC280" class="line" lang="plaintext"> * Code related to read parsing was completely rewritten to improve</span>
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281
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<pre style="margin: 0;">+<span id="LC281" class="line" lang="plaintext"> scalability to many threads. In short, the critical section is</span>
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282
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<pre style="margin: 0;">+<span id="LC282" class="line" lang="plaintext"> simpler and parses input reads in batches rather than one at a time.</span>
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283
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<pre style="margin: 0;">+<span id="LC283" class="line" lang="plaintext"> The improvement applies to all read formats.</span>
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284
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<pre style="margin: 0;">+<span id="LC284" class="line" lang="plaintext"> * TBB is now the default threading library. We consistently found TBB to give</span>
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285
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<pre style="margin: 0;">+<span id="LC285" class="line" lang="plaintext"> superior thread scaling. It is widely available and widely installed.</span>
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286
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<pre style="margin: 0;">+<span id="LC286" class="line" lang="plaintext"> That said, we are also preserving a "legacy" version of Bowtie that,</span>
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287
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<pre style="margin: 0;">+<span id="LC287" class="line" lang="plaintext"> like previous releases, does not use TBB. To compile Bowtie source</span>
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<pre style="margin: 0;">+<span id="LC288" class="line" lang="plaintext"> in legacy mode use `NO_TBB=1`. To</span>
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289
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<pre style="margin: 0;">+<span id="LC289" class="line" lang="plaintext"> use legacy binaries, download the appropriate binary archive with</span>
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290
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<pre style="margin: 0;">+<span id="LC290" class="line" lang="plaintext"> "legacy" in the name.</span>
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291
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<pre style="margin: 0;">+<span id="LC291" class="line" lang="plaintext"> * Bowtie now uses a queue-based lock rather</span>
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292
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<pre style="margin: 0;">+<span id="LC292" class="line" lang="plaintext"> than a spin or heavyweight lock. We find this gives superior thread</span>
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293
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<pre style="margin: 0;">+<span id="LC293" class="line" lang="plaintext"> scaling; we saw an order-of-magnitude throughput improvements at</span>
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294
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<pre style="margin: 0;">+<span id="LC294" class="line" lang="plaintext"> 120 threads in one experiment, for example.</span>
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295
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<pre style="margin: 0;">+<span id="LC295" class="line" lang="plaintext"> * Unnecessary thread synchronization removed</span>
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296
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<pre style="margin: 0;">+<span id="LC296" class="line" lang="plaintext"> * Fixed issue with parsing FASTA records with greater-than symbol in the name</span>
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297
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<pre style="margin: 0;">+<span id="LC297" class="line" lang="plaintext"> * Now detects and reports inconsistencies between `--score-min` and `--ma`</span>
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298
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<pre style="margin: 0;">+<span id="LC298" class="line" lang="plaintext"> * Changed default for `--bmaxdivn` to yield better memory footprint and running time when building an index with many threads</span>
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299
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<pre style="margin: 0;">+<span id="LC299" class="line" lang="plaintext"></span>
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300
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<pre style="margin: 0;">+<span id="LC300" class="line" lang="plaintext">## Version 2.2.9 - Apr 22, 2016 ##</span>
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301
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<pre style="margin: 0;">+<span id="LC301" class="line" lang="plaintext"></span>
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302
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<pre style="margin: 0;">+<span id="LC302" class="line" lang="plaintext"> * Fixed the multiple threads issue for the bowtie2-build.</span>
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303
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<pre style="margin: 0;">+<span id="LC303" class="line" lang="plaintext"> * Fixed a TBB related build issue impacting TBB v4.4.</span>
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304
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<pre style="margin: 0;">+<span id="LC304" class="line" lang="plaintext"></span>
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305
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<pre style="margin: 0;">+<span id="LC305" class="line" lang="plaintext">## Version 2.2.8 - Mar 10, 2016 ##</span>
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306
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<pre style="margin: 0;">+<span id="LC306" class="line" lang="plaintext"></span>
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307
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<pre style="margin: 0;">+<span id="LC307" class="line" lang="plaintext"> * Various website updates.</span>
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308
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<pre style="margin: 0;">+<span id="LC308" class="line" lang="plaintext"> * Fixed the bowtie2-build issue that made TBB compilation fail.</span>
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309
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<pre style="margin: 0;">+<span id="LC309" class="line" lang="plaintext"> * Fixed the static build for Win32 platform.</span>
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310
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<pre style="margin: 0;">+<span id="LC310" class="line" lang="plaintext"></span>
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311
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<pre style="margin: 0;">+<span id="LC311" class="line" lang="plaintext"></span>
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312
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<pre style="margin: 0;">+<span id="LC312" class="line" lang="plaintext">## Version 2.2.7 - Feb 10, 2016 ##</span>
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313
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<pre style="margin: 0;">+<span id="LC313" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC314" class="line" lang="plaintext"> * Added a parallel index build option: bowtie2-build --threads <# threads>.</span>
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315
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<pre style="margin: 0;">+<span id="LC315" class="line" lang="plaintext"> * Fixed an issue whereby IUPAC codes (other than A/C/G/T/N) in reads were</span>
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316
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<pre style="margin: 0;">+<span id="LC316" class="line" lang="plaintext"> converted to As. Now all non-A/C/G/T characters in reads become Ns.</span>
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317
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<pre style="margin: 0;">+<span id="LC317" class="line" lang="plaintext"> * Fixed some compilation issues, including for the Intel C++ Compiler.</span>
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318
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<pre style="margin: 0;">+<span id="LC318" class="line" lang="plaintext"> * Removed debugging code that could impede performance for many alignment</span>
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319
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<pre style="margin: 0;">+<span id="LC319" class="line" lang="plaintext"> threads.</span>
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320
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<pre style="margin: 0;">+<span id="LC320" class="line" lang="plaintext"> * Fixed a few typos in documentation.</span>
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321
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<pre style="margin: 0;">+<span id="LC321" class="line" lang="plaintext"></span>
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322
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<pre style="margin: 0;">+<span id="LC322" class="line" lang="plaintext">## Version 2.2.6 - Jul 22, 2015 ##</span>
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323
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<pre style="margin: 0;">+<span id="LC323" class="line" lang="plaintext"></span>
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324
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<pre style="margin: 0;">+<span id="LC324" class="line" lang="plaintext"> * Switched to a stable sort to avoid some potential reproducibility confusions.</span>
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325
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<pre style="margin: 0;">+<span id="LC325" class="line" lang="plaintext"> * Added 'install' target for *nix platforms.</span>
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326
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<pre style="margin: 0;">+<span id="LC326" class="line" lang="plaintext"> * Added the Intel TBB option which provides in most situations a better performance</span>
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327
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<pre style="margin: 0;">+<span id="LC327" class="line" lang="plaintext"> output. TBB is not present by default in the current build but can be added</span>
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328
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<pre style="margin: 0;">+<span id="LC328" class="line" lang="plaintext"> by compiling the source code with WITH_TBB=1 option.</span>
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329
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<pre style="margin: 0;">+<span id="LC329" class="line" lang="plaintext"> * Fixed a bug that caused seed lenght to be dependent of the -L and -N parameters order.</span>
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330
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<pre style="margin: 0;">+<span id="LC330" class="line" lang="plaintext"> * Fixed a bug that caused --local followed by -N to reset seed lenght to 22 which is</span>
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331
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<pre style="margin: 0;">+<span id="LC331" class="line" lang="plaintext"> actually the default value for global.</span>
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332
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<pre style="margin: 0;">+<span id="LC332" class="line" lang="plaintext"> * Enable compilation on FreeBSD and clang, although gmake port is still required.</span>
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333
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<pre style="margin: 0;">+<span id="LC333" class="line" lang="plaintext"> * Fixed an issue that made bowtie2 compilation process to fail on Snow Leopard.</span>
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334
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<pre style="margin: 0;">+<span id="LC334" class="line" lang="plaintext"></span>
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335
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<pre style="margin: 0;">+<span id="LC335" class="line" lang="plaintext"></span>
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336
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<pre style="margin: 0;">+<span id="LC336" class="line" lang="plaintext">## Version 2.2.5 - Mar 9, 2015 ##</span>
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337
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<pre style="margin: 0;">+<span id="LC337" class="line" lang="plaintext"></span>
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338
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<pre style="margin: 0;">+<span id="LC338" class="line" lang="plaintext"> * Fixed some situations where incorrectly we could detect a Mavericks platform.</span>
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339
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<pre style="margin: 0;">+<span id="LC339" class="line" lang="plaintext"> * Fixed some manual issues including some HTML bad formating.</span>
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340
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<pre style="margin: 0;">+<span id="LC340" class="line" lang="plaintext"> * Make sure the wrapper correctly identifies the platform under OSX.</span>
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341
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<pre style="margin: 0;">+<span id="LC341" class="line" lang="plaintext"> * Fixed --rg/--rg-id options where included spaces were incorrectly treated.</span>
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342
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<pre style="margin: 0;">+<span id="LC342" class="line" lang="plaintext"> * Various documentation fixes added by contributors.</span>
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343
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<pre style="margin: 0;">+<span id="LC343" class="line" lang="plaintext"> * Fixed the incorrect behavior where parameter file names may contain spaces.</span>
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344
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<pre style="margin: 0;">+<span id="LC344" class="line" lang="plaintext"> * Fixed bugs related with the presence of spaces in the path where bowtie binaries are stored.</span>
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345
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<pre style="margin: 0;">+<span id="LC345" class="line" lang="plaintext"> * Improved exception handling for missformated quality values.</span>
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346
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<pre style="margin: 0;">+<span id="LC346" class="line" lang="plaintext"> * Improved redundancy checks by correctly account for soft clipping.</span>
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347
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<pre style="margin: 0;">+<span id="LC347" class="line" lang="plaintext"></span>
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348
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<pre style="margin: 0;">+<span id="LC348" class="line" lang="plaintext">## Version 2.2.4 - Oct 22, 2014 ##</span>
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349
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<pre style="margin: 0;">+<span id="LC349" class="line" lang="plaintext"></span>
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350
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<pre style="margin: 0;">+<span id="LC350" class="line" lang="plaintext"> * Fixed a Mavericks OSX specific bug caused by some linkage ambiguities.</span>
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351
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<pre style="margin: 0;">+<span id="LC351" class="line" lang="plaintext"> * Added lz4 compression option for the wrapper.</span>
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352
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<pre style="margin: 0;">+<span id="LC352" class="line" lang="plaintext"> * Fixed the vanishing --no-unal help line.</span>
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353
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<pre style="margin: 0;">+<span id="LC353" class="line" lang="plaintext"> * Added the static linkage for MinGW builds.</span>
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354
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<pre style="margin: 0;">+<span id="LC354" class="line" lang="plaintext"> * Added extra seed-hit output.</span>
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355
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<pre style="margin: 0;">+<span id="LC355" class="line" lang="plaintext"> * Fixed missing 0-length read in fastq --passthrough output.</span>
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356
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<pre style="margin: 0;">+<span id="LC356" class="line" lang="plaintext"> * Fixed an issue that would cause different output in -a mode depending on random seed.</span>
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357
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<pre style="margin: 0;">+<span id="LC357" class="line" lang="plaintext"></span>
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358
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<pre style="margin: 0;">+<span id="LC358" class="line" lang="plaintext">## Version 2.2.3 - May 30, 2014 ##</span>
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359
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<pre style="margin: 0;">+<span id="LC359" class="line" lang="plaintext"></span>
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360
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<pre style="margin: 0;">+<span id="LC360" class="line" lang="plaintext"> * Fixed a bug that made loading an index into memory crash sometimes.</span>
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361
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<pre style="margin: 0;">+<span id="LC361" class="line" lang="plaintext"> * Fixed a silent failure to warn the user in case the -x option is missing.</span>
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362
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<pre style="margin: 0;">+<span id="LC362" class="line" lang="plaintext"> * Updated al, un, al-conc and un-conc options to avoid confusion in cases</span>
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363
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<pre style="margin: 0;">+<span id="LC363" class="line" lang="plaintext"> where the user does not provide a base file name.</span>
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364
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<pre style="margin: 0;">+<span id="LC364" class="line" lang="plaintext"> * Fixed a spurious assert that made bowtie2-inspect debug fail.</span>
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365
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<pre style="margin: 0;">+<span id="LC365" class="line" lang="plaintext"></span>
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366
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<pre style="margin: 0;">+<span id="LC366" class="line" lang="plaintext">## Version 2.2.2 - April 10, 2014 ##</span>
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367
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<pre style="margin: 0;">+<span id="LC367" class="line" lang="plaintext"></span>
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368
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<pre style="margin: 0;">+<span id="LC368" class="line" lang="plaintext"> * Improved performance for cases where the reference contains ambiguous</span>
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369
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<pre style="margin: 0;">+<span id="LC369" class="line" lang="plaintext"> or masked nucleobases represented by Ns.</span>
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370
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<pre style="margin: 0;">+<span id="LC370" class="line" lang="plaintext"></span>
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371
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<pre style="margin: 0;">+<span id="LC371" class="line" lang="plaintext">## Version 2.2.1 - February 28, 2014 ##</span>
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372
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<pre style="margin: 0;">+<span id="LC372" class="line" lang="plaintext"></span>
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373
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<pre style="margin: 0;">+<span id="LC373" class="line" lang="plaintext"> * Improved way in which index files are loaded for alignment. Should fix</span>
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374
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<pre style="margin: 0;">+<span id="LC374" class="line" lang="plaintext"> efficiency problems on some filesystems.</span>
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375
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<pre style="margin: 0;">+<span id="LC375" class="line" lang="plaintext"> * Fixed a bug that made older systems unable to correctly deal with bowtie</span>
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376
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<pre style="margin: 0;">+<span id="LC376" class="line" lang="plaintext"> relative symbolic links.</span>
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377
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<pre style="margin: 0;">+<span id="LC377" class="line" lang="plaintext"> * Fixed a bug that, for very big indexes, could determine to determine file</span>
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378
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<pre style="margin: 0;">+<span id="LC378" class="line" lang="plaintext"> offsets correctly.</span>
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379
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<pre style="margin: 0;">+<span id="LC379" class="line" lang="plaintext"> * Fixed a bug where using --no-unal option incorrectly suppressed</span>
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380
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<pre style="margin: 0;">+<span id="LC380" class="line" lang="plaintext"> --un/--un-conc output.</span>
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381
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<pre style="margin: 0;">+<span id="LC381" class="line" lang="plaintext"> * Dropped a perl dependency that could cause problems on old systems.</span>
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382
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<pre style="margin: 0;">+<span id="LC382" class="line" lang="plaintext"> * Added --no-1mm-upfront option and clarified documentation for parameters</span>
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383
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<pre style="margin: 0;">+<span id="LC383" class="line" lang="plaintext"> governing the multiseed heuristic.</span>
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384
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<pre style="margin: 0;">+<span id="LC384" class="line" lang="plaintext"></span>
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385
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<pre style="margin: 0;">+<span id="LC385" class="line" lang="plaintext">## Version 2.2.0 - February 10, 2014 ##</span>
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386
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<pre style="margin: 0;">+<span id="LC386" class="line" lang="plaintext"></span>
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387
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<pre style="margin: 0;">+<span id="LC387" class="line" lang="plaintext"> * Improved index querying efficiency using "population count" instructions</span>
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388
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<pre style="margin: 0;">+<span id="LC388" class="line" lang="plaintext"> available since SSE4.2.</span>
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389
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<pre style="margin: 0;">+<span id="LC389" class="line" lang="plaintext"> * Added support for large and small indexes, removing 4-billion-nucleotide</span>
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390
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<pre style="margin: 0;">+<span id="LC390" class="line" lang="plaintext"> barrier. Bowtie 2 can now be used with reference genomes of any size.</span>
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391
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<pre style="margin: 0;">+<span id="LC391" class="line" lang="plaintext"> * Fixed bug that could cause bowtie2-build to crash when reference length</span>
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392
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<pre style="margin: 0;">+<span id="LC392" class="line" lang="plaintext"> is close to 4 billion.</span>
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393
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<pre style="margin: 0;">+<span id="LC393" class="line" lang="plaintext"> * Fixed issue in bowtie2-inspect that caused -e mode not to output</span>
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394
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<pre style="margin: 0;">+<span id="LC394" class="line" lang="plaintext"> nucleotides properly.</span>
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395
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<pre style="margin: 0;">+<span id="LC395" class="line" lang="plaintext"> * Added a CL: string to the @PG SAM header to preserve information about</span>
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396
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<pre style="margin: 0;">+<span id="LC396" class="line" lang="plaintext"> the aligner binary and paramteres.</span>
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397
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<pre style="margin: 0;">+<span id="LC397" class="line" lang="plaintext"> * No longer releasing 32-bit binaries. Simplified manual and Makefile</span>
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398
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<pre style="margin: 0;">+<span id="LC398" class="line" lang="plaintext"> accordingly.</span>
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399
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<pre style="margin: 0;">+<span id="LC399" class="line" lang="plaintext"> * Credits to the Intel(r) enabling team for performance optimizations</span>
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400
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<pre style="margin: 0;">+<span id="LC400" class="line" lang="plaintext"> included in this release. Thank you!</span>
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401
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<pre style="margin: 0;">+<span id="LC401" class="line" lang="plaintext"> * Phased out CygWin support.</span>
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402
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<pre style="margin: 0;">+<span id="LC402" class="line" lang="plaintext"> * Added the .bat generation for Windows.</span>
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403
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<pre style="margin: 0;">+<span id="LC403" class="line" lang="plaintext"> * Fixed some issues with some uncommon chars in fasta files.</span>
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404
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<pre style="margin: 0;">+<span id="LC404" class="line" lang="plaintext"> * Fixed wrappers so bowtie can now be used with symlinks.</span>
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353
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405
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<pre style="margin: 0;"> <span id="LC405" class="line" lang="plaintext"></span>
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354
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406
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<pre style="margin: 0;"> <span id="LC406" class="line" lang="plaintext">Bowtie 2 on GitHub - February 4, 2014</span>
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355
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<pre style="margin: 0;">-<span id="LC355" class="line" lang="plaintext"> * Bowtie 2 source now lives in a public GitHub repository:</span>
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356
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<pre style="margin: 0;">-<span id="LC356" class="line" lang="plaintext"> https://github.com/BenLangmead/bowtie2.</span>
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357
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<pre style="margin: 0;">-<span id="LC357" class="line" lang="plaintext"></span>
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358
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<pre style="margin: 0;">-<span id="LC358" class="line" lang="plaintext">Version 2.1.0 - February 21, 2013</span>
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359
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<pre style="margin: 0;">-<span id="LC359" class="line" lang="plaintext"> * Improved multithreading support so that Bowtie 2 now uses native Windows</span>
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360
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<pre style="margin: 0;">-<span id="LC360" class="line" lang="plaintext"> threads when compiled on Windows and uses a faster mutex. Threading</span>
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361
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<pre style="margin: 0;">-<span id="LC361" class="line" lang="plaintext"> performance should improve on all platforms.</span>
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362
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<pre style="margin: 0;">-<span id="LC362" class="line" lang="plaintext"> * Improved support for building 64-bit binaries for Windows x64 platforms.</span>
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363
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<pre style="margin: 0;">-<span id="LC363" class="line" lang="plaintext"> * Bowtie is using a spinlocking mechanism by default. </span>
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364
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<pre style="margin: 0;">-<span id="LC364" class="line" lang="plaintext"> * Test option --nospin is no longer available. However bowtie2 can always</span>
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365
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<pre style="margin: 0;">-<span id="LC365" class="line" lang="plaintext"> be recompiled with EXTRA_FLAGS="-DNO_SPINLOCK" in order to drop the </span>
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<pre style="margin: 0;">-<span id="LC366" class="line" lang="plaintext"> default spinlock usage.</span>
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<pre style="margin: 0;">-<span id="LC367" class="line" lang="plaintext"></span>
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368
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<pre style="margin: 0;">-<span id="LC368" class="line" lang="plaintext">Version 2.0.6 - January 27, 2013</span>
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369
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<pre style="margin: 0;">-<span id="LC369" class="line" lang="plaintext"> * Fixed issue whereby spurious output would be written in --no-unal mode.</span>
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370
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<pre style="margin: 0;">-<span id="LC370" class="line" lang="plaintext"> * Fixed issue whereby multiple input files combined with --reorder would</span>
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371
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<pre style="margin: 0;">-<span id="LC371" class="line" lang="plaintext"> cause truncated output and a memory spike.</span>
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372
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<pre style="margin: 0;">-<span id="LC372" class="line" lang="plaintext"> * Fixed spinlock datatype for Win64 API (LLP64 data model) which made it</span>
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373
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<pre style="margin: 0;">-<span id="LC373" class="line" lang="plaintext"> crash when compiled under Windows 7 x64.</span>
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374
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<pre style="margin: 0;">-<span id="LC374" class="line" lang="plaintext"> * Fixed bowtie2 wrapper to handle filename/paths operations in a more </span>
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375
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<pre style="margin: 0;">-<span id="LC375" class="line" lang="plaintext"> platform independent manner.</span>
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376
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<pre style="margin: 0;">-<span id="LC376" class="line" lang="plaintext"> * Added pthread as a default library option under cygwin, and pthreadGC</span>
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377
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<pre style="margin: 0;">-<span id="LC377" class="line" lang="plaintext"> for MinGW.</span>
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378
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<pre style="margin: 0;">-<span id="LC378" class="line" lang="plaintext"> * Fixed some minor issues that made MinGW compilation fail.</span>
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379
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<pre style="margin: 0;">-<span id="LC379" class="line" lang="plaintext"></span>
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380
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<pre style="margin: 0;">-<span id="LC380" class="line" lang="plaintext">Version 2.0.5 - January 4, 2013</span>
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381
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<pre style="margin: 0;">-<span id="LC381" class="line" lang="plaintext"> * Fixed an issue that would cause excessive memory allocation when aligning</span>
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382
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<pre style="margin: 0;">-<span id="LC382" class="line" lang="plaintext"> to very repetitive genomes.</span>
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383
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<pre style="margin: 0;">-<span id="LC383" class="line" lang="plaintext"> * Fixed an issue that would cause a pseudo-randomness-related assert to be</span>
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384
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<pre style="margin: 0;">-<span id="LC384" class="line" lang="plaintext"> thrown in debug mode under rare circumstances.</span>
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385
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<pre style="margin: 0;">-<span id="LC385" class="line" lang="plaintext"> * When bowtie2-build fails, it will now delete index files created so far so</span>
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386
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<pre style="margin: 0;">-<span id="LC386" class="line" lang="plaintext"> that invalid index files don't linger.</span>
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387
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<pre style="margin: 0;">-<span id="LC387" class="line" lang="plaintext"> * Tokenizer no longer has limit of 10,000 tokens, which was a problem for</span>
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388
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<pre style="margin: 0;">-<span id="LC388" class="line" lang="plaintext"> users trying to index a very large number of FASTA files.</span>
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389
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<pre style="margin: 0;">-<span id="LC389" class="line" lang="plaintext"> * Updated manual's discussion of the -I and -X options to mention that</span>
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390
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<pre style="margin: 0;">-<span id="LC390" class="line" lang="plaintext"> setting them farther apart makes Bowtie 2 slower.</span>
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391
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<pre style="margin: 0;">-<span id="LC391" class="line" lang="plaintext"> * Renamed COPYING to LICENSE and created a README to be GitHub-friendly.</span>
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<pre style="margin: 0;">-<span id="LC392" class="line" lang="plaintext"></span>
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393
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<pre style="margin: 0;">-<span id="LC393" class="line" lang="plaintext">Version 2.0.4 - December 17, 2012</span>
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394
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<pre style="margin: 0;">-<span id="LC394" class="line" lang="plaintext"> * Fixed issue whereby --un, --al, --un-conc and --al-conc options would</span>
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395
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<pre style="margin: 0;">-<span id="LC395" class="line" lang="plaintext"> incorrectly suppress SAM output.</span>
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396
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<pre style="margin: 0;">-<span id="LC396" class="line" lang="plaintext"> * Fixed minor command-line parsing issue in wrapper script.</span>
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397
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<pre style="margin: 0;">-<span id="LC397" class="line" lang="plaintext"> * Fixed issue on Windows where wrapper script would fail to find</span>
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398
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<pre style="margin: 0;">-<span id="LC398" class="line" lang="plaintext"> bowtie2-align.exe binary.</span>
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399
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<pre style="margin: 0;">-<span id="LC399" class="line" lang="plaintext"> * Updated some of the index-building scripts and documentation.</span>
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400
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<pre style="margin: 0;">-<span id="LC400" class="line" lang="plaintext"> * Updated author's contact info in usage message.</span>
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401
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<pre style="margin: 0;">-<span id="LC401" class="line" lang="plaintext"></span>
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402
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<pre style="margin: 0;">-<span id="LC402" class="line" lang="plaintext">Version 2.0.3 - December 14, 2012</span>
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403
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<pre style="margin: 0;">-<span id="LC403" class="line" lang="plaintext"> * Fixed thread safely issues that could cause crashes with a large number of</span>
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404
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<pre style="margin: 0;">-<span id="LC404" class="line" lang="plaintext"> threads. Thanks to John O'Neill for identifying these issues.</span>
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405
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<pre style="margin: 0;">-<span id="LC405" class="line" lang="plaintext"> * Fixed some problems with pseudo-random number generation that could cause</span>
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406
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<pre style="margin: 0;">-<span id="LC406" class="line" lang="plaintext"> unequal distribution of alignments across equally good candidate loci.</span>
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407
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<pre style="margin: 0;">-<span id="LC407" class="line" lang="plaintext"> * The --un, --al, --un-conc, and --al-conc options (and their compressed</span>
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408
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<pre style="margin: 0;">-<span id="LC408" class="line" lang="plaintext"> analogs) are all much faster now, making it less likely that they become</span>
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409
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<pre style="margin: 0;">-<span id="LC409" class="line" lang="plaintext"> the bottleneck when Bowtie 2 is run with large -p.</span>
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410
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<pre style="margin: 0;">-<span id="LC410" class="line" lang="plaintext"> * Fixed issue with innaccurate mapping qualities, XS:i, and YS:i flags when</span>
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<td class="old_line diff-line-num old" data-linenumber="411" 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">
411
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<pre style="margin: 0;">-<span id="LC411" class="line" lang="plaintext"> --no-mixed and --no-discordant are specified at the same time.</span>
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<td class="old_line diff-line-num old" data-linenumber="412" 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">
412
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<pre style="margin: 0;">-<span id="LC412" class="line" lang="plaintext"> * Fixed some compiler warnings and errors when using clang++ to compile.</span>
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<td class="old_line diff-line-num old" data-linenumber="413" 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">
413
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<pre style="margin: 0;">-<span id="LC413" class="line" lang="plaintext"> * Fixed race condition in bowtie2 script when named pipes are used.</span>
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<td class="old_line diff-line-num old" data-linenumber="414" 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">
414
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<pre style="margin: 0;">-<span id="LC414" class="line" lang="plaintext"> * Added more discussion of whitespace in read names to manual.</span>
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415
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<pre style="margin: 0;">-<span id="LC415" class="line" lang="plaintext"></span>
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416
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<pre style="margin: 0;">-<span id="LC416" class="line" lang="plaintext">Version 2.0.2 - October 31, 2012</span>
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417
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<pre style="margin: 0;">-<span id="LC417" class="line" lang="plaintext"> * Fixes a couple small issues pointed out to me immediately after 2.0.1</span>
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<pre style="margin: 0;">-<span id="LC418" class="line" lang="plaintext"> release</span>
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<pre style="margin: 0;">-<span id="LC419" class="line" lang="plaintext"> * Mac binaries now built on 10.6 in order to be forward-compatible with more</span>
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420
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<pre style="margin: 0;">-<span id="LC420" class="line" lang="plaintext"> Mac OS versions</span>
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<pre style="margin: 0;">-<span id="LC421" class="line" lang="plaintext"> * Small changes to source to make it compile with gcc versions up to 4.7</span>
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422
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<pre style="margin: 0;">-<span id="LC422" class="line" lang="plaintext"> without warnings</span>
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<pre style="margin: 0;">-<span id="LC423" class="line" lang="plaintext"></span>
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424
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<pre style="margin: 0;">-<span id="LC424" class="line" lang="plaintext">Version 2.0.1 - October 31, 2012</span>
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<pre style="margin: 0;">-<span id="LC425" class="line" lang="plaintext"> * First non-beta release.</span>
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426
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<pre style="margin: 0;">-<span id="LC426" class="line" lang="plaintext"> * Fixed an issue that would cause Bowtie 2 to use excessive amounts of</span>
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427
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<pre style="margin: 0;">-<span id="LC427" class="line" lang="plaintext"> memory for closely-matching and highly repetitive reads under some</span>
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428
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<pre style="margin: 0;">-<span id="LC428" class="line" lang="plaintext"> circumstances.</span>
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429
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<pre style="margin: 0;">-<span id="LC429" class="line" lang="plaintext"> * Fixed a bug in --mm mode that would fail to report when an index file</span>
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430
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<pre style="margin: 0;">-<span id="LC430" class="line" lang="plaintext"> could not be memory-mapped.</span>
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431
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<pre style="margin: 0;">-<span id="LC431" class="line" lang="plaintext"> * Added --non-deterministic option, which better matches how some users</span>
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432
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<pre style="margin: 0;">-<span id="LC432" class="line" lang="plaintext"> expect the pseudo-random generator inside Bowtie 2 to work. Normally, if</span>
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433
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<pre style="margin: 0;">-<span id="LC433" class="line" lang="plaintext"> you give the same read (same name, sequence and qualities) and --seed, you</span>
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434
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<pre style="margin: 0;">-<span id="LC434" class="line" lang="plaintext"> get the same answer. --non-deterministic breaks that guarantee. This can</span>
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435
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<pre style="margin: 0;">-<span id="LC435" class="line" lang="plaintext"> be more appropriate for datasets where the input contains many identical</span>
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436
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<pre style="margin: 0;">-<span id="LC436" class="line" lang="plaintext"> reads (same name, same sequence, same qualities).</span>
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437
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<pre style="margin: 0;">-<span id="LC437" class="line" lang="plaintext"> * Fixed a bug in bowtie2-build would yield corrupt index files when memory</span>
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438
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<pre style="margin: 0;">-<span id="LC438" class="line" lang="plaintext"> settings were adjusted in the middle of indexing.</span>
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439
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<pre style="margin: 0;">-<span id="LC439" class="line" lang="plaintext"> * Clarified in manual that --un (or --un-*) options print reads exactly as</span>
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440
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<pre style="margin: 0;">-<span id="LC440" class="line" lang="plaintext"> they appeared in the input, and that they are not necessarily written in</span>
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441
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<pre style="margin: 0;">-<span id="LC441" class="line" lang="plaintext"> the same order as they appeared in the input.</span>
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442
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<pre style="margin: 0;">-<span id="LC442" class="line" lang="plaintext"> * Fixed issue whereby wrapper would incorrectly interpret arguments with</span>
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443
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<pre style="margin: 0;">-<span id="LC443" class="line" lang="plaintext"> --al as a prefix (e.g. --all) as --al.</span>
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<pre style="margin: 0;">-<span id="LC444" class="line" lang="plaintext"> * Added option --omit-sec-seq, which causes Bowtie 2 to set SEQ and QUAL</span>
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<pre style="margin: 0;">-<span id="LC445" class="line" lang="plaintext"> fields to "*" for secondary alignments.</span>
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<pre style="margin: 0;">-<span id="LC446" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC447" class="line" lang="plaintext">Version 2.0.0-beta7 - July 9, 2012</span>
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<pre style="margin: 0;">-<span id="LC448" class="line" lang="plaintext"> * Fixed an issue in how Bowtie 2 aligns longer reads in --local mode. Some</span>
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<pre style="margin: 0;">-<span id="LC449" class="line" lang="plaintext"> alignments were incorrectly curtailed on the left-hand side.</span>
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<pre style="margin: 0;">-<span id="LC450" class="line" lang="plaintext"> * Fixed issue --un (or --un-*) would fail to output unaligned reads when</span>
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<pre style="margin: 0;">-<span id="LC451" class="line" lang="plaintext"> --no-unal was also specified.</span>
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<pre style="margin: 0;">-<span id="LC452" class="line" lang="plaintext"> * Fixed issue whereby --un-* were significantly slowing down Bowtie 2 when</span>
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<pre style="margin: 0;">-<span id="LC453" class="line" lang="plaintext"> -p was set greater than 1.</span>
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<pre style="margin: 0;">-<span id="LC454" class="line" lang="plaintext"> * Fixed issue that would could cause hangs in -a mode or when -k is set</span>
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<pre style="margin: 0;">-<span id="LC455" class="line" lang="plaintext"> high.</span>
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<pre style="margin: 0;">-<span id="LC456" class="line" lang="plaintext"> * Fixed issue whereby the SAM FLAGS field could be set incorrectly for</span>
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<pre style="margin: 0;">-<span id="LC457" class="line" lang="plaintext"> secondary paired-end alignments with -a or -k > 1.</span>
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<pre style="margin: 0;">-<span id="LC458" class="line" lang="plaintext"> * When input reads are unpaired, Bowtie 2 no longer removes the trailing /1</span>
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459
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<pre style="margin: 0;">-<span id="LC459" class="line" lang="plaintext"> or /2 from the read name.</span>
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<pre style="margin: 0;">-<span id="LC460" class="line" lang="plaintext"> * -M option is now deprecated. It will be removed in subsequent versions.</span>
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<pre style="margin: 0;">-<span id="LC461" class="line" lang="plaintext"> What used to be called -M mode is still the default mode, and -k and -a</span>
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<pre style="margin: 0;">-<span id="LC462" class="line" lang="plaintext"> are still there alternatives to the default mode, but adjusting the -M</span>
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<pre style="margin: 0;">-<span id="LC463" class="line" lang="plaintext"> setting is deprecated. Use the -D and -R options to adjust the effort</span>
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<pre style="margin: 0;">-<span id="LC464" class="line" lang="plaintext"> expended to find valid alignments.</span>
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<pre style="margin: 0;">-<span id="LC465" class="line" lang="plaintext"> * Gaps are now left-aligned in a manner similar to BWA and other tools.</span>
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466
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<pre style="margin: 0;">-<span id="LC466" class="line" lang="plaintext"> * Fixed issue whereby wrapper script would not pass on exitlevel correctly,</span>
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467
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<pre style="margin: 0;">-<span id="LC467" class="line" lang="plaintext"> sometimes spuriously hiding non-0 exitlevel.</span>
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<pre style="margin: 0;">-<span id="LC468" class="line" lang="plaintext"> * Added documentation for YT:Z to manual.</span>
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<pre style="margin: 0;">-<span id="LC469" class="line" lang="plaintext"> * Fixed documentation describing how Bowtie 2 searches for an index given an</span>
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<pre style="margin: 0;">-<span id="LC470" class="line" lang="plaintext"> index basename.</span>
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<pre style="margin: 0;">-<span id="LC471" class="line" lang="plaintext"> * Fixed inconsistent documentation for the default value of the -i parameter</span>
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<pre style="margin: 0;">-<span id="LC472" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC473" class="line" lang="plaintext">Version 2.0.0-beta6 - May 7, 2012</span>
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<pre style="margin: 0;">-<span id="LC474" class="line" lang="plaintext"> * Bowtie 2 now handles longer reads in a more memory-economical fashion,</span>
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475
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<pre style="margin: 0;">-<span id="LC475" class="line" lang="plaintext"> which should prevent many out-of-memory issues for longer reads.</span>
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<pre style="margin: 0;">-<span id="LC476" class="line" lang="plaintext"> * Error message now produced when -L is set greater than 32.</span>
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477
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<pre style="margin: 0;">-<span id="LC477" class="line" lang="plaintext"> * Added a warning message to warn when bowtie2-align binary is being run</span>
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478
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<pre style="margin: 0;">-<span id="LC478" class="line" lang="plaintext"> directly, rather than via the wrapper. Some functionality is provided by</span>
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<pre style="margin: 0;">-<span id="LC479" class="line" lang="plaintext"> the wrapper, so Bowtie 2 should always be run via the bowtie2 executable</span>
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480
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<pre style="margin: 0;">-<span id="LC480" class="line" lang="plaintext"> rather than bowtie2-align.</span>
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481
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<pre style="margin: 0;">-<span id="LC481" class="line" lang="plaintext"> * Fixed an occasional crashing bug that was usually caused by setting the</span>
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<pre style="margin: 0;">-<span id="LC482" class="line" lang="plaintext"> seed length relatively short.</span>
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<pre style="margin: 0;">-<span id="LC483" class="line" lang="plaintext"> * Fixed an issue whereby the FLAG, RNEXT and PNEXT fields were incorrect for</span>
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<pre style="margin: 0;">-<span id="LC484" class="line" lang="plaintext"> some paired-end alignments. Specifically, this affected paired-end</span>
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<pre style="margin: 0;">-<span id="LC485" class="line" lang="plaintext"> alignments where both mates aligned and one or both mates aligned</span>
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486
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<pre style="margin: 0;">-<span id="LC486" class="line" lang="plaintext"> non-uniquely.</span>
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487
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<pre style="margin: 0;">-<span id="LC487" class="line" lang="plaintext"> * Fixed issue whereby compressed input would sometimes be mishandled.</span>
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488
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<pre style="margin: 0;">-<span id="LC488" class="line" lang="plaintext"> * Renamed --sam-* options to omit the "sam-" prefix for brevity. The old</span>
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489
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<pre style="margin: 0;">-<span id="LC489" class="line" lang="plaintext"> option names will also work.</span>
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490
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<pre style="margin: 0;">-<span id="LC490" class="line" lang="plaintext"> * Added --no-unal option to suppress SAM records corresponding to unaligned</span>
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491
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<pre style="margin: 0;">-<span id="LC491" class="line" lang="plaintext"> reads, i.e., records where FLAG field has 0x4 set.</span>
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492
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<pre style="margin: 0;">-<span id="LC492" class="line" lang="plaintext"> * Added --rg-id option and enhanced the documentation for both --rg-id and</span>
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493
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<pre style="margin: 0;">-<span id="LC493" class="line" lang="plaintext"> --rg. Users were confused by the need to specify --rg "ID:(something)" in</span>
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494
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<pre style="margin: 0;">-<span id="LC494" class="line" lang="plaintext"> order for the @RG line to be printed; hopefully this is clearer now.</span>
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495
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<pre style="margin: 0;">-<span id="LC495" class="line" lang="plaintext"> * Index updates: indexes linked to in the right-hand sidebar have been</span>
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<pre style="margin: 0;">-<span id="LC496" class="line" lang="plaintext"> updated to include the unplaced contigs appearing in the UCSC "random"</span>
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497
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<pre style="margin: 0;">-<span id="LC497" class="line" lang="plaintext"> FASTA files. This makes the indexes more complete. Also, an index for</span>
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498
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<pre style="margin: 0;">-<span id="LC498" class="line" lang="plaintext"> the latest mouse assembly, mm10 (AKA "GRCm38") has been added.</span>
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499
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<pre style="margin: 0;">-<span id="LC499" class="line" lang="plaintext"></span>
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500
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<pre style="margin: 0;">-<span id="LC500" class="line" lang="plaintext">Version 2.0.0-beta5 - December 14, 2011</span>
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501
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<pre style="margin: 0;">-<span id="LC501" class="line" lang="plaintext"> * Added --un, --al, --un-conc, and --al-conc options that write unpaired</span>
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502
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<pre style="margin: 0;">-<span id="LC502" class="line" lang="plaintext"> and/or paired-end reads to files depending on whether they align at least</span>
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503
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<pre style="margin: 0;">-<span id="LC503" class="line" lang="plaintext"> once or fail to align.</span>
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504
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<pre style="margin: 0;">-<span id="LC504" class="line" lang="plaintext"> * Added --reorder option. When enabled, the order of the SAM records output</span>
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505
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<pre style="margin: 0;">-<span id="LC505" class="line" lang="plaintext"> by Bowtie 2 will match the order of the input reads even when -p is set</span>
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506
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<pre style="margin: 0;">-<span id="LC506" class="line" lang="plaintext"> greater than 1. This is disabled by default; enabling it makes Bowtie 2</span>
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507
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<pre style="margin: 0;">-<span id="LC507" class="line" lang="plaintext"> somewhat slower and use somewhat more memory when -p is set greater than</span>
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508
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<pre style="margin: 0;">-<span id="LC508" class="line" lang="plaintext"> 1.</span>
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509
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<pre style="margin: 0;">-<span id="LC509" class="line" lang="plaintext"> * Changed the default --score-min in --local mode to G,20,8. This ought to</span>
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510
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<pre style="margin: 0;">-<span id="LC510" class="line" lang="plaintext"> improve sensitivity and accuracy in many cases.</span>
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511
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<pre style="margin: 0;">-<span id="LC511" class="line" lang="plaintext"> * Improved error reporting.</span>
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512
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<pre style="margin: 0;">-<span id="LC512" class="line" lang="plaintext"> * Fixed some minor documentation issues.</span>
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513
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<pre style="margin: 0;">-<span id="LC513" class="line" lang="plaintext"> * Note: I am aware of an issue whereby longer reads (>10,000 bp) drive the</span>
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514
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<pre style="margin: 0;">-<span id="LC514" class="line" lang="plaintext"> memory footprint way up and often cause an out-of-memory exception. This</span>
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515
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<pre style="margin: 0;">-<span id="LC515" class="line" lang="plaintext"> will be fixed in a future version.</span>
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516
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<pre style="margin: 0;">-<span id="LC516" class="line" lang="plaintext"></span>
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517
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<pre style="margin: 0;">-<span id="LC517" class="line" lang="plaintext">Version 2.0.0-beta4 - December 5, 2011</span>
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518
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<pre style="margin: 0;">-<span id="LC518" class="line" lang="plaintext"> * Accuracy improvements.</span>
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519
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<pre style="margin: 0;">-<span id="LC519" class="line" lang="plaintext"> * Speed improvements in some situations.</span>
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520
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<pre style="margin: 0;">-<span id="LC520" class="line" lang="plaintext"> * Fixed a handful of crashing bugs.</span>
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521
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<pre style="margin: 0;">-<span id="LC521" class="line" lang="plaintext"> * Fixed some documentation bugs.</span>
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522
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<pre style="margin: 0;">-<span id="LC522" class="line" lang="plaintext"> * Fixed bug whereby --version worked incorrectly.</span>
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523
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<pre style="margin: 0;">-<span id="LC523" class="line" lang="plaintext"> * Fixed formatting bug with MD:Z optional field that would sometimes fail to</span>
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524
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<pre style="margin: 0;">-<span id="LC524" class="line" lang="plaintext"> follow a mismatch with a number.</span>
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525
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<pre style="margin: 0;">-<span id="LC525" class="line" lang="plaintext"> * Added -D option for controlling the maximum number of seed extensions that</span>
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526
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<pre style="margin: 0;">-<span id="LC526" class="line" lang="plaintext"> can fail in a row before we move on. This option or something like it</span>
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527
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<pre style="margin: 0;">-<span id="LC527" class="line" lang="plaintext"> will eventually replace the argument to -M.</span>
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528
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<pre style="margin: 0;">-<span id="LC528" class="line" lang="plaintext"> * Added -R option to control maximum number of times re-seeding is attempted</span>
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529
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<pre style="margin: 0;">-<span id="LC529" class="line" lang="plaintext"> for a read with repetitive seeds.</span>
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530
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<pre style="margin: 0;">-<span id="LC530" class="line" lang="plaintext"> * Changed default to --no-dovetail. Specifying --dovetail turns it back on.</span>
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531
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<pre style="margin: 0;">-<span id="LC531" class="line" lang="plaintext"> * Added second argument for --mp option so that user can set maximum and</span>
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532
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<pre style="margin: 0;">-<span id="LC532" class="line" lang="plaintext"> minimum mismatch penalties at once. Also tweaked the formula for</span>
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533
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<pre style="margin: 0;">-<span id="LC533" class="line" lang="plaintext"> calculating the quality-aware mismatch penalty.</span>
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534
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<pre style="margin: 0;">-<span id="LC534" class="line" lang="plaintext"></span>
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535
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<pre style="margin: 0;">-<span id="LC535" class="line" lang="plaintext">Version 2.0.0-beta3 - November 1, 2011</span>
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536
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<pre style="margin: 0;">-<span id="LC536" class="line" lang="plaintext"> * Accuracy improvements.</span>
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537
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<pre style="margin: 0;">-<span id="LC537" class="line" lang="plaintext"> * Speed improvements in some situations.</span>
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538
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<pre style="margin: 0;">-<span id="LC538" class="line" lang="plaintext"> * Fixed a handful of crashing bugs.</span>
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539
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<pre style="margin: 0;">-<span id="LC539" class="line" lang="plaintext"> * Fixed a bug whereby number of repetitively aligned reads could be</span>
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540
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<pre style="margin: 0;">-<span id="LC540" class="line" lang="plaintext"> misreported in the summary output.</span>
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541
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<pre style="margin: 0;">-<span id="LC541" class="line" lang="plaintext"></span>
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542
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<pre style="margin: 0;">-<span id="LC542" class="line" lang="plaintext">Version 2.0.0-beta2 - October 16, 2011</span>
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543
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<td class="new_line diff-line-num old" data-linenumber="407" 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="LC543" class="line" lang="plaintext"> * Added manual, both included in the download package and on the website.</span>
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544
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<pre style="margin: 0;">-<span id="LC544" class="line" lang="plaintext"> The website will always have the manual for the latest version.</span>
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<td class="old_line diff-line-num old" data-linenumber="545" 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">
545
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<pre style="margin: 0;">-<span id="LC545" class="line" lang="plaintext"> * Added Linux 32-bit and 64-bit binary packages. Mac OS X packages to come.</span>
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546
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<pre style="margin: 0;">-<span id="LC546" class="line" lang="plaintext"> Still working on a Windows package.</span>
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<td class="old_line diff-line-num old" data-linenumber="547" 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">
547
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<pre style="margin: 0;">-<span id="LC547" class="line" lang="plaintext"> * Fixed a bug that led to crashes when seed-alignment result memory was</span>
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<pre style="margin: 0;">-<span id="LC548" class="line" lang="plaintext"> exhausted.</span>
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<pre style="margin: 0;">-<span id="LC549" class="line" lang="plaintext"> * Changed the --end-to-end mode --score-min default to be less permissive.</span>
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<pre style="margin: 0;">-<span id="LC550" class="line" lang="plaintext"> The previous threshold seemed to be having an adverse effect on accuracy,</span>
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<pre style="margin: 0;">-<span id="LC551" class="line" lang="plaintext"> though the fix implemented in this version comes at the expense of some</span>
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<pre style="margin: 0;">-<span id="LC552" class="line" lang="plaintext"> sensitivity.</span>
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<pre style="margin: 0;">-<span id="LC553" class="line" lang="plaintext"> * Changed the --end-to-end mode -M default to be lower by 2 notches. This</span>
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<pre style="margin: 0;">-<span id="LC554" class="line" lang="plaintext"> offsets any detrimental effect that the previous change would have had on</span>
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<pre style="margin: 0;">-<span id="LC555" class="line" lang="plaintext"> speed, without a large adverse impact on accuracy. As always, setting -M</span>
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<pre style="margin: 0;">-<span id="LC556" class="line" lang="plaintext"> higher will yield still greater accuracy at the expense of speed.</span>
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<pre style="margin: 0;">-<span id="LC557" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC558" class="line" lang="plaintext">Version 2.0.0-beta1 - September 22, 2011</span>
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559
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<pre style="margin: 0;">-<span id="LC559" class="line" lang="plaintext"> * First public release.</span>
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<pre style="margin: 0;">-<span id="LC560" class="line" lang="plaintext"> * Caveats: as of now, the manual is incomplete, there's no tutorial, and no</span>
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<pre style="margin: 0;">-<span id="LC561" class="line" lang="plaintext"> example genome or example reads. All these will be fixed in upcoming</span>
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<pre style="margin: 0;">-<span id="LC562" class="line" lang="plaintext"> releases.</span>
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<pre style="margin: 0;">-<span id="LC563" class="line" lang="plaintext"> * Only a source package is currently available. Platform-specific binaries</span>
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<pre style="margin: 0;">-<span id="LC564" class="line" lang="plaintext"> will be included in future releases.</span></pre>
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<pre style="margin: 0;">+<span id="LC407" class="line" lang="plaintext"> * Bowtie 2 source now lives in a public GitHub repository:</span>
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408
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<pre style="margin: 0;">+<span id="LC408" class="line" lang="plaintext"> https://github.com/BenLangmead/bowtie2.</span>
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409
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<pre style="margin: 0;">+<span id="LC409" class="line" lang="plaintext"></span>
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410
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<pre style="margin: 0;">+<span id="LC410" class="line" lang="plaintext">## Version 2.1.0 - February 21, 2013 ##</span>
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411
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<pre style="margin: 0;">+<span id="LC411" class="line" lang="plaintext"></span>
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412
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<pre style="margin: 0;">+<span id="LC412" class="line" lang="plaintext"> * Improved multithreading support so that Bowtie 2 now uses native Windows</span>
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413
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<pre style="margin: 0;">+<span id="LC413" class="line" lang="plaintext"> threads when compiled on Windows and uses a faster mutex. Threading</span>
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414
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<pre style="margin: 0;">+<span id="LC414" class="line" lang="plaintext"> performance should improve on all platforms.</span>
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415
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<pre style="margin: 0;">+<span id="LC415" class="line" lang="plaintext"> * Improved support for building 64-bit binaries for Windows x64 platforms.</span>
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416
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<pre style="margin: 0;">+<span id="LC416" class="line" lang="plaintext"> * Bowtie is using a spinlocking mechanism by default.</span>
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417
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<pre style="margin: 0;">+<span id="LC417" class="line" lang="plaintext"> * Test option --nospin is no longer available. However bowtie2 can always</span>
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418
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<pre style="margin: 0;">+<span id="LC418" class="line" lang="plaintext"> be recompiled with EXTRA_FLAGS="-DNO_SPINLOCK" in order to drop the</span>
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419
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<pre style="margin: 0;">+<span id="LC419" class="line" lang="plaintext"> default spinlock usage.</span>
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420
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<pre style="margin: 0;">+<span id="LC420" class="line" lang="plaintext"></span>
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421
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<pre style="margin: 0;">+<span id="LC421" class="line" lang="plaintext">## Version 2.0.6 - January 27, 2013 ##</span>
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422
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<pre style="margin: 0;">+<span id="LC422" class="line" lang="plaintext"></span>
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423
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<pre style="margin: 0;">+<span id="LC423" class="line" lang="plaintext"> * Fixed issue whereby spurious output would be written in --no-unal mode.</span>
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424
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<pre style="margin: 0;">+<span id="LC424" class="line" lang="plaintext"> * Fixed issue whereby multiple input files combined with --reorder would</span>
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425
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<pre style="margin: 0;">+<span id="LC425" class="line" lang="plaintext"> cause truncated output and a memory spike.</span>
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426
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<pre style="margin: 0;">+<span id="LC426" class="line" lang="plaintext"> * Fixed spinlock datatype for Win64 API (LLP64 data model) which made it</span>
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427
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<pre style="margin: 0;">+<span id="LC427" class="line" lang="plaintext"> crash when compiled under Windows 7 x64.</span>
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428
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<pre style="margin: 0;">+<span id="LC428" class="line" lang="plaintext"> * Fixed bowtie2 wrapper to handle filename/paths operations in a more</span>
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429
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<pre style="margin: 0;">+<span id="LC429" class="line" lang="plaintext"> platform independent manner.</span>
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430
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<pre style="margin: 0;">+<span id="LC430" class="line" lang="plaintext"> * Added pthread as a default library option under cygwin, and pthreadGC</span>
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431
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<pre style="margin: 0;">+<span id="LC431" class="line" lang="plaintext"> for MinGW.</span>
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432
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<pre style="margin: 0;">+<span id="LC432" class="line" lang="plaintext"> * Fixed some minor issues that made MinGW compilation fail.</span>
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433
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<pre style="margin: 0;">+<span id="LC433" class="line" lang="plaintext"></span>
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434
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<pre style="margin: 0;">+<span id="LC434" class="line" lang="plaintext">## Version 2.0.5 - January 4, 2013 ##</span>
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435
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<pre style="margin: 0;">+<span id="LC435" class="line" lang="plaintext"></span>
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436
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<pre style="margin: 0;">+<span id="LC436" class="line" lang="plaintext"> * Fixed an issue that would cause excessive memory allocation when aligning</span>
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437
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<pre style="margin: 0;">+<span id="LC437" class="line" lang="plaintext"> to very repetitive genomes.</span>
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438
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<pre style="margin: 0;">+<span id="LC438" class="line" lang="plaintext"> * Fixed an issue that would cause a pseudo-randomness-related assert to be</span>
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439
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<pre style="margin: 0;">+<span id="LC439" class="line" lang="plaintext"> thrown in debug mode under rare circumstances.</span>
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440
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<pre style="margin: 0;">+<span id="LC440" class="line" lang="plaintext"> * When bowtie2-build fails, it will now delete index files created so far so</span>
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441
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<pre style="margin: 0;">+<span id="LC441" class="line" lang="plaintext"> that invalid index files don't linger.</span>
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442
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<pre style="margin: 0;">+<span id="LC442" class="line" lang="plaintext"> * Tokenizer no longer has limit of 10,000 tokens, which was a problem for</span>
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443
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<pre style="margin: 0;">+<span id="LC443" class="line" lang="plaintext"> users trying to index a very large number of FASTA files.</span>
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444
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<pre style="margin: 0;">+<span id="LC444" class="line" lang="plaintext"> * Updated manual's discussion of the -I and -X options to mention that</span>
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445
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<pre style="margin: 0;">+<span id="LC445" class="line" lang="plaintext"> setting them farther apart makes Bowtie 2 slower.</span>
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446
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<pre style="margin: 0;">+<span id="LC446" class="line" lang="plaintext"> * Renamed COPYING to LICENSE and created a README to be GitHub-friendly.</span>
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447
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<pre style="margin: 0;">+<span id="LC447" class="line" lang="plaintext"></span>
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448
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<pre style="margin: 0;">+<span id="LC448" class="line" lang="plaintext">## Version 2.0.4 - December 17, 2012 ##</span>
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449
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<pre style="margin: 0;">+<span id="LC449" class="line" lang="plaintext"></span>
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450
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<pre style="margin: 0;">+<span id="LC450" class="line" lang="plaintext"> * Fixed issue whereby --un, --al, --un-conc and --al-conc options would</span>
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451
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<pre style="margin: 0;">+<span id="LC451" class="line" lang="plaintext"> incorrectly suppress SAM output.</span>
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452
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<pre style="margin: 0;">+<span id="LC452" class="line" lang="plaintext"> * Fixed minor command-line parsing issue in wrapper script.</span>
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453
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<pre style="margin: 0;">+<span id="LC453" class="line" lang="plaintext"> * Fixed issue on Windows where wrapper script would fail to find</span>
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454
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<pre style="margin: 0;">+<span id="LC454" class="line" lang="plaintext"> bowtie2-align.exe binary.</span>
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<pre style="margin: 0;">+<span id="LC455" class="line" lang="plaintext"> * Updated some of the index-building scripts and documentation.</span>
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456
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<pre style="margin: 0;">+<span id="LC456" class="line" lang="plaintext"> * Updated author's contact info in usage message.</span>
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457
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<pre style="margin: 0;">+<span id="LC457" class="line" lang="plaintext"></span>
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458
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<pre style="margin: 0;">+<span id="LC458" class="line" lang="plaintext">## Version 2.0.3 - December 14, 2012 ##</span>
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459
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<pre style="margin: 0;">+<span id="LC459" class="line" lang="plaintext"></span>
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460
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<pre style="margin: 0;">+<span id="LC460" class="line" lang="plaintext"> * Fixed thread safely issues that could cause crashes with a large number of</span>
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461
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<pre style="margin: 0;">+<span id="LC461" class="line" lang="plaintext"> threads. Thanks to John O'Neill for identifying these issues.</span>
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462
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<pre style="margin: 0;">+<span id="LC462" class="line" lang="plaintext"> * Fixed some problems with pseudo-random number generation that could cause</span>
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463
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<pre style="margin: 0;">+<span id="LC463" class="line" lang="plaintext"> unequal distribution of alignments across equally good candidate loci.</span>
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<pre style="margin: 0;">+<span id="LC464" class="line" lang="plaintext"> * The --un, --al, --un-conc, and --al-conc options (and their compressed</span>
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465
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<pre style="margin: 0;">+<span id="LC465" class="line" lang="plaintext"> analogs) are all much faster now, making it less likely that they become</span>
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<pre style="margin: 0;">+<span id="LC466" class="line" lang="plaintext"> the bottleneck when Bowtie 2 is run with large -p.</span>
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<pre style="margin: 0;">+<span id="LC467" class="line" lang="plaintext"> * Fixed issue with innaccurate mapping qualities, XS:i, and YS:i flags when</span>
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468
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<pre style="margin: 0;">+<span id="LC468" class="line" lang="plaintext"> --no-mixed and --no-discordant are specified at the same time.</span>
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469
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<pre style="margin: 0;">+<span id="LC469" class="line" lang="plaintext"> * Fixed some compiler warnings and errors when using clang++ to compile.</span>
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470
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<pre style="margin: 0;">+<span id="LC470" class="line" lang="plaintext"> * Fixed race condition in bowtie2 script when named pipes are used.</span>
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471
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<pre style="margin: 0;">+<span id="LC471" class="line" lang="plaintext"> * Added more discussion of whitespace in read names to manual.</span>
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472
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<pre style="margin: 0;">+<span id="LC472" class="line" lang="plaintext"></span>
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473
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<pre style="margin: 0;">+<span id="LC473" class="line" lang="plaintext">## Version 2.0.2 - October 31, 2012 ##</span>
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474
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<pre style="margin: 0;">+<span id="LC474" class="line" lang="plaintext"></span>
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475
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<pre style="margin: 0;">+<span id="LC475" class="line" lang="plaintext"> * Fixes a couple small issues pointed out to me immediately after 2.0.1</span>
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476
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<pre style="margin: 0;">+<span id="LC476" class="line" lang="plaintext"> release</span>
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477
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<pre style="margin: 0;">+<span id="LC477" class="line" lang="plaintext"> * Mac binaries now built on 10.6 in order to be forward-compatible with more</span>
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478
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<pre style="margin: 0;">+<span id="LC478" class="line" lang="plaintext"> Mac OS versions</span>
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479
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<pre style="margin: 0;">+<span id="LC479" class="line" lang="plaintext"> * Small changes to source to make it compile with gcc versions up to 4.7</span>
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480
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<pre style="margin: 0;">+<span id="LC480" class="line" lang="plaintext"> without warnings</span>
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481
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<pre style="margin: 0;">+<span id="LC481" class="line" lang="plaintext"></span>
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482
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<pre style="margin: 0;">+<span id="LC482" class="line" lang="plaintext">## Version 2.0.1 - October 31, 2012 ##</span>
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483
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<pre style="margin: 0;">+<span id="LC483" class="line" lang="plaintext"></span>
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484
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<pre style="margin: 0;">+<span id="LC484" class="line" lang="plaintext"> * First non-beta release.</span>
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485
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<pre style="margin: 0;">+<span id="LC485" class="line" lang="plaintext"> * Fixed an issue that would cause Bowtie 2 to use excessive amounts of</span>
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486
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<pre style="margin: 0;">+<span id="LC486" class="line" lang="plaintext"> memory for closely-matching and highly repetitive reads under some</span>
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487
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<pre style="margin: 0;">+<span id="LC487" class="line" lang="plaintext"> circumstances.</span>
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488
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<pre style="margin: 0;">+<span id="LC488" class="line" lang="plaintext"> * Fixed a bug in --mm mode that would fail to report when an index file</span>
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489
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<pre style="margin: 0;">+<span id="LC489" class="line" lang="plaintext"> could not be memory-mapped.</span>
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490
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<pre style="margin: 0;">+<span id="LC490" class="line" lang="plaintext"> * Added --non-deterministic option, which better matches how some users</span>
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491
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<pre style="margin: 0;">+<span id="LC491" class="line" lang="plaintext"> expect the pseudo-random generator inside Bowtie 2 to work. Normally, if</span>
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492
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<pre style="margin: 0;">+<span id="LC492" class="line" lang="plaintext"> you give the same read (same name, sequence and qualities) and --seed, you</span>
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493
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<pre style="margin: 0;">+<span id="LC493" class="line" lang="plaintext"> get the same answer. --non-deterministic breaks that guarantee. This can</span>
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494
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<pre style="margin: 0;">+<span id="LC494" class="line" lang="plaintext"> be more appropriate for datasets where the input contains many identical</span>
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495
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<pre style="margin: 0;">+<span id="LC495" class="line" lang="plaintext"> reads (same name, same sequence, same qualities).</span>
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496
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<pre style="margin: 0;">+<span id="LC496" class="line" lang="plaintext"> * Fixed a bug in bowtie2-build would yield corrupt index files when memory</span>
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497
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<pre style="margin: 0;">+<span id="LC497" class="line" lang="plaintext"> settings were adjusted in the middle of indexing.</span>
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498
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<pre style="margin: 0;">+<span id="LC498" class="line" lang="plaintext"> * Clarified in manual that --un (or --un-*) options print reads exactly as</span>
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499
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<pre style="margin: 0;">+<span id="LC499" class="line" lang="plaintext"> they appeared in the input, and that they are not necessarily written in</span>
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500
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<pre style="margin: 0;">+<span id="LC500" class="line" lang="plaintext"> the same order as they appeared in the input.</span>
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501
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<pre style="margin: 0;">+<span id="LC501" class="line" lang="plaintext"> * Fixed issue whereby wrapper would incorrectly interpret arguments with</span>
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502
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<pre style="margin: 0;">+<span id="LC502" class="line" lang="plaintext"> --al as a prefix (e.g. --all) as --al.</span>
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503
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<pre style="margin: 0;">+<span id="LC503" class="line" lang="plaintext"> * Added option --omit-sec-seq, which causes Bowtie 2 to set SEQ and QUAL</span>
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504
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<pre style="margin: 0;">+<span id="LC504" class="line" lang="plaintext"> fields to "*" for secondary alignments.</span>
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505
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<pre style="margin: 0;">+<span id="LC505" class="line" lang="plaintext"></span>
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506
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<pre style="margin: 0;">+<span id="LC506" class="line" lang="plaintext">## Version 2.0.0-beta7 - July 9, 2012 ##</span>
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507
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<pre style="margin: 0;">+<span id="LC507" class="line" lang="plaintext"></span>
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508
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<pre style="margin: 0;">+<span id="LC508" class="line" lang="plaintext"> * Fixed an issue in how Bowtie 2 aligns longer reads in --local mode. Some</span>
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509
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<pre style="margin: 0;">+<span id="LC509" class="line" lang="plaintext"> alignments were incorrectly curtailed on the left-hand side.</span>
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510
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<pre style="margin: 0;">+<span id="LC510" class="line" lang="plaintext"> * Fixed issue --un (or --un-*) would fail to output unaligned reads when</span>
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511
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<pre style="margin: 0;">+<span id="LC511" class="line" lang="plaintext"> --no-unal was also specified.</span>
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512
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<pre style="margin: 0;">+<span id="LC512" class="line" lang="plaintext"> * Fixed issue whereby --un-* were significantly slowing down Bowtie 2 when</span>
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513
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<pre style="margin: 0;">+<span id="LC513" class="line" lang="plaintext"> -p was set greater than 1.</span>
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514
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<pre style="margin: 0;">+<span id="LC514" class="line" lang="plaintext"> * Fixed issue that would could cause hangs in -a mode or when -k is set</span>
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515
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<pre style="margin: 0;">+<span id="LC515" class="line" lang="plaintext"> high.</span>
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516
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<pre style="margin: 0;">+<span id="LC516" class="line" lang="plaintext"> * Fixed issue whereby the SAM FLAGS field could be set incorrectly for</span>
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517
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<pre style="margin: 0;">+<span id="LC517" class="line" lang="plaintext"> secondary paired-end alignments with -a or -k > 1.</span>
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518
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<pre style="margin: 0;">+<span id="LC518" class="line" lang="plaintext"> * When input reads are unpaired, Bowtie 2 no longer removes the trailing /1</span>
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519
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<pre style="margin: 0;">+<span id="LC519" class="line" lang="plaintext"> or /2 from the read name.</span>
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520
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<pre style="margin: 0;">+<span id="LC520" class="line" lang="plaintext"> * -M option is now deprecated. It will be removed in subsequent versions.</span>
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521
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<pre style="margin: 0;">+<span id="LC521" class="line" lang="plaintext"> What used to be called -M mode is still the default mode, and -k and -a</span>
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522
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<pre style="margin: 0;">+<span id="LC522" class="line" lang="plaintext"> are still there alternatives to the default mode, but adjusting the -M</span>
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523
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<pre style="margin: 0;">+<span id="LC523" class="line" lang="plaintext"> setting is deprecated. Use the -D and -R options to adjust the effort</span>
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524
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<pre style="margin: 0;">+<span id="LC524" class="line" lang="plaintext"> expended to find valid alignments.</span>
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525
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<pre style="margin: 0;">+<span id="LC525" class="line" lang="plaintext"> * Gaps are now left-aligned in a manner similar to BWA and other tools.</span>
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526
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<pre style="margin: 0;">+<span id="LC526" class="line" lang="plaintext"> * Fixed issue whereby wrapper script would not pass on exitlevel correctly,</span>
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527
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<pre style="margin: 0;">+<span id="LC527" class="line" lang="plaintext"> sometimes spuriously hiding non-0 exitlevel.</span>
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528
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<pre style="margin: 0;">+<span id="LC528" class="line" lang="plaintext"> * Added documentation for YT:Z to manual.</span>
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529
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<pre style="margin: 0;">+<span id="LC529" class="line" lang="plaintext"> * Fixed documentation describing how Bowtie 2 searches for an index given an</span>
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530
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<pre style="margin: 0;">+<span id="LC530" class="line" lang="plaintext"> index basename.</span>
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531
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<pre style="margin: 0;">+<span id="LC531" class="line" lang="plaintext"> * Fixed inconsistent documentation for the default value of the -i parameter</span>
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532
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<pre style="margin: 0;">+<span id="LC532" class="line" lang="plaintext"></span>
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533
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<pre style="margin: 0;">+<span id="LC533" class="line" lang="plaintext">## Version 2.0.0-beta6 - May 7, 2012 ##</span>
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534
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<pre style="margin: 0;">+<span id="LC534" class="line" lang="plaintext"></span>
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535
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<pre style="margin: 0;">+<span id="LC535" class="line" lang="plaintext"> * Bowtie 2 now handles longer reads in a more memory-economical fashion,</span>
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536
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<pre style="margin: 0;">+<span id="LC536" class="line" lang="plaintext"> which should prevent many out-of-memory issues for longer reads.</span>
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537
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<pre style="margin: 0;">+<span id="LC537" class="line" lang="plaintext"> * Error message now produced when -L is set greater than 32.</span>
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538
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<pre style="margin: 0;">+<span id="LC538" class="line" lang="plaintext"> * Added a warning message to warn when bowtie2-align binary is being run</span>
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539
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<pre style="margin: 0;">+<span id="LC539" class="line" lang="plaintext"> directly, rather than via the wrapper. Some functionality is provided by</span>
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540
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<pre style="margin: 0;">+<span id="LC540" class="line" lang="plaintext"> the wrapper, so Bowtie 2 should always be run via the bowtie2 executable</span>
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541
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<pre style="margin: 0;">+<span id="LC541" class="line" lang="plaintext"> rather than bowtie2-align.</span>
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542
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<pre style="margin: 0;">+<span id="LC542" class="line" lang="plaintext"> * Fixed an occasional crashing bug that was usually caused by setting the</span>
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543
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<pre style="margin: 0;">+<span id="LC543" class="line" lang="plaintext"> seed length relatively short.</span>
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544
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<pre style="margin: 0;">+<span id="LC544" class="line" lang="plaintext"> * Fixed an issue whereby the FLAG, RNEXT and PNEXT fields were incorrect for</span>
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545
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<pre style="margin: 0;">+<span id="LC545" class="line" lang="plaintext"> some paired-end alignments. Specifically, this affected paired-end</span>
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546
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<pre style="margin: 0;">+<span id="LC546" class="line" lang="plaintext"> alignments where both mates aligned and one or both mates aligned</span>
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547
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<pre style="margin: 0;">+<span id="LC547" class="line" lang="plaintext"> non-uniquely.</span>
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548
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<pre style="margin: 0;">+<span id="LC548" class="line" lang="plaintext"> * Fixed issue whereby compressed input would sometimes be mishandled.</span>
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549
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<pre style="margin: 0;">+<span id="LC549" class="line" lang="plaintext"> * Renamed --sam-* options to omit the "sam-" prefix for brevity. The old</span>
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550
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<pre style="margin: 0;">+<span id="LC550" class="line" lang="plaintext"> option names will also work.</span>
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551
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<pre style="margin: 0;">+<span id="LC551" class="line" lang="plaintext"> * Added --no-unal option to suppress SAM records corresponding to unaligned</span>
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552
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<pre style="margin: 0;">+<span id="LC552" class="line" lang="plaintext"> reads, i.e., records where FLAG field has 0x4 set.</span>
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553
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<pre style="margin: 0;">+<span id="LC553" class="line" lang="plaintext"> * Added --rg-id option and enhanced the documentation for both --rg-id and</span>
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554
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<pre style="margin: 0;">+<span id="LC554" class="line" lang="plaintext"> --rg. Users were confused by the need to specify --rg "ID:(something)" in</span>
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555
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<pre style="margin: 0;">+<span id="LC555" class="line" lang="plaintext"> order for the @RG line to be printed; hopefully this is clearer now.</span>
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556
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<pre style="margin: 0;">+<span id="LC556" class="line" lang="plaintext"> * Index updates: indexes linked to in the right-hand sidebar have been</span>
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557
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<pre style="margin: 0;">+<span id="LC557" class="line" lang="plaintext"> updated to include the unplaced contigs appearing in the UCSC "random"</span>
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558
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<pre style="margin: 0;">+<span id="LC558" class="line" lang="plaintext"> FASTA files. This makes the indexes more complete. Also, an index for</span>
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559
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<pre style="margin: 0;">+<span id="LC559" class="line" lang="plaintext"> the latest mouse assembly, mm10 (AKA "GRCm38") has been added.</span>
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560
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<pre style="margin: 0;">+<span id="LC560" class="line" lang="plaintext"></span>
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561
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<pre style="margin: 0;">+<span id="LC561" class="line" lang="plaintext">## Version 2.0.0-beta5 - December 14, 2011 ##</span>
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562
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<pre style="margin: 0;">+<span id="LC562" class="line" lang="plaintext"></span>
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563
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<pre style="margin: 0;">+<span id="LC563" class="line" lang="plaintext"> * Added --un, --al, --un-conc, and --al-conc options that write unpaired</span>
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564
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<pre style="margin: 0;">+<span id="LC564" class="line" lang="plaintext"> and/or paired-end reads to files depending on whether they align at least</span>
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565
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<pre style="margin: 0;">+<span id="LC565" class="line" lang="plaintext"> once or fail to align.</span>
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566
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<pre style="margin: 0;">+<span id="LC566" class="line" lang="plaintext"> * Added --reorder option. When enabled, the order of the SAM records output</span>
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567
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<pre style="margin: 0;">+<span id="LC567" class="line" lang="plaintext"> by Bowtie 2 will match the order of the input reads even when -p is set</span>
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568
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<pre style="margin: 0;">+<span id="LC568" class="line" lang="plaintext"> greater than 1. This is disabled by default; enabling it makes Bowtie 2</span>
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569
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<pre style="margin: 0;">+<span id="LC569" class="line" lang="plaintext"> somewhat slower and use somewhat more memory when -p is set greater than</span>
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570
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<pre style="margin: 0;">+<span id="LC570" class="line" lang="plaintext"> 1.</span>
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571
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<pre style="margin: 0;">+<span id="LC571" class="line" lang="plaintext"> * Changed the default --score-min in --local mode to G,20,8. This ought to</span>
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572
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<pre style="margin: 0;">+<span id="LC572" class="line" lang="plaintext"> improve sensitivity and accuracy in many cases.</span>
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573
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<pre style="margin: 0;">+<span id="LC573" class="line" lang="plaintext"> * Improved error reporting.</span>
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574
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<pre style="margin: 0;">+<span id="LC574" class="line" lang="plaintext"> * Fixed some minor documentation issues.</span>
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575
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<pre style="margin: 0;">+<span id="LC575" class="line" lang="plaintext"> * Note: I am aware of an issue whereby longer reads (>10,000 bp) drive the</span>
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576
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<pre style="margin: 0;">+<span id="LC576" class="line" lang="plaintext"> memory footprint way up and often cause an out-of-memory exception. This</span>
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577
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<pre style="margin: 0;">+<span id="LC577" class="line" lang="plaintext"> will be fixed in a future version.</span>
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578
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<pre style="margin: 0;">+<span id="LC578" class="line" lang="plaintext"></span>
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579
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<pre style="margin: 0;">+<span id="LC579" class="line" lang="plaintext">## Version 2.0.0-beta4 - December 5, 2011 ##</span>
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580
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<pre style="margin: 0;">+<span id="LC580" class="line" lang="plaintext"></span>
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581
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<pre style="margin: 0;">+<span id="LC581" class="line" lang="plaintext"> * Accuracy improvements.</span>
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582
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<pre style="margin: 0;">+<span id="LC582" class="line" lang="plaintext"> * Speed improvements in some situations.</span>
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583
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<pre style="margin: 0;">+<span id="LC583" class="line" lang="plaintext"> * Fixed a handful of crashing bugs.</span>
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584
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<pre style="margin: 0;">+<span id="LC584" class="line" lang="plaintext"> * Fixed some documentation bugs.</span>
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585
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<pre style="margin: 0;">+<span id="LC585" class="line" lang="plaintext"> * Fixed bug whereby --version worked incorrectly.</span>
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586
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<pre style="margin: 0;">+<span id="LC586" class="line" lang="plaintext"> * Fixed formatting bug with MD:Z optional field that would sometimes fail to</span>
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587
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<pre style="margin: 0;">+<span id="LC587" class="line" lang="plaintext"> follow a mismatch with a number.</span>
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588
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<pre style="margin: 0;">+<span id="LC588" class="line" lang="plaintext"> * Added -D option for controlling the maximum number of seed extensions that</span>
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589
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<pre style="margin: 0;">+<span id="LC589" class="line" lang="plaintext"> can fail in a row before we move on. This option or something like it</span>
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590
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<pre style="margin: 0;">+<span id="LC590" class="line" lang="plaintext"> will eventually replace the argument to -M.</span>
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591
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<pre style="margin: 0;">+<span id="LC591" class="line" lang="plaintext"> * Added -R option to control maximum number of times re-seeding is attempted</span>
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592
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<pre style="margin: 0;">+<span id="LC592" class="line" lang="plaintext"> for a read with repetitive seeds.</span>
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593
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<pre style="margin: 0;">+<span id="LC593" class="line" lang="plaintext"> * Changed default to --no-dovetail. Specifying --dovetail turns it back on.</span>
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594
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<pre style="margin: 0;">+<span id="LC594" class="line" lang="plaintext"> * Added second argument for --mp option so that user can set maximum and</span>
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595
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<pre style="margin: 0;">+<span id="LC595" class="line" lang="plaintext"> minimum mismatch penalties at once. Also tweaked the formula for</span>
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596
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<pre style="margin: 0;">+<span id="LC596" class="line" lang="plaintext"> calculating the quality-aware mismatch penalty.</span>
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597
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<pre style="margin: 0;">+<span id="LC597" class="line" lang="plaintext"></span>
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598
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<pre style="margin: 0;">+<span id="LC598" class="line" lang="plaintext">## Version 2.0.0-beta3 - November 1, 2011 ##</span>
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599
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<pre style="margin: 0;">+<span id="LC599" class="line" lang="plaintext"></span>
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600
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<pre style="margin: 0;">+<span id="LC600" class="line" lang="plaintext"> * Accuracy improvements.</span>
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601
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<pre style="margin: 0;">+<span id="LC601" class="line" lang="plaintext"> * Speed improvements in some situations.</span>
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602
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<pre style="margin: 0;">+<span id="LC602" class="line" lang="plaintext"> * Fixed a handful of crashing bugs.</span>
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603
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<pre style="margin: 0;">+<span id="LC603" class="line" lang="plaintext"> * Fixed a bug whereby number of repetitively aligned reads could be</span>
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604
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<pre style="margin: 0;">+<span id="LC604" class="line" lang="plaintext"> misreported in the summary output.</span>
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605
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<pre style="margin: 0;">+<span id="LC605" class="line" lang="plaintext"></span>
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606
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<pre style="margin: 0;">+<span id="LC606" class="line" lang="plaintext">## Version 2.0.0-beta2 - October 16, 2011 ##</span>
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607
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<pre style="margin: 0;">+<span id="LC607" class="line" lang="plaintext"></span>
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608
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<pre style="margin: 0;">+<span id="LC608" class="line" lang="plaintext"> * Added manual, both included in the download package and on the website.</span>
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609
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<pre style="margin: 0;">+<span id="LC609" class="line" lang="plaintext"> The website will always have the manual for the latest version.</span>
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<td class="new_line diff-line-num new" data-linenumber="610" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
610
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<pre style="margin: 0;">+<span id="LC610" class="line" lang="plaintext"> * Added Linux 32-bit and 64-bit binary packages. Mac OS X packages to come.</span>
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611
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<pre style="margin: 0;">+<span id="LC611" class="line" lang="plaintext"> Still working on a Windows package.</span>
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612
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<pre style="margin: 0;">+<span id="LC612" class="line" lang="plaintext"> * Fixed a bug that led to crashes when seed-alignment result memory was</span>
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613
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<pre style="margin: 0;">+<span id="LC613" class="line" lang="plaintext"> exhausted.</span>
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614
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<pre style="margin: 0;">+<span id="LC614" class="line" lang="plaintext"> * Changed the --end-to-end mode --score-min default to be less permissive.</span>
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615
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<pre style="margin: 0;">+<span id="LC615" class="line" lang="plaintext"> The previous threshold seemed to be having an adverse effect on accuracy,</span>
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616
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<pre style="margin: 0;">+<span id="LC616" class="line" lang="plaintext"> though the fix implemented in this version comes at the expense of some</span>
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617
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<pre style="margin: 0;">+<span id="LC617" class="line" lang="plaintext"> sensitivity.</span>
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<td class="new_line diff-line-num new" data-linenumber="618" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
618
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<pre style="margin: 0;">+<span id="LC618" class="line" lang="plaintext"> * Changed the --end-to-end mode -M default to be lower by 2 notches. This</span>
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<td class="new_line diff-line-num new" data-linenumber="619" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
619
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<pre style="margin: 0;">+<span id="LC619" class="line" lang="plaintext"> offsets any detrimental effect that the previous change would have had on</span>
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620
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<pre style="margin: 0;">+<span id="LC620" class="line" lang="plaintext"> speed, without a large adverse impact on accuracy. As always, setting -M</span>
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<pre style="margin: 0;">+<span id="LC621" class="line" lang="plaintext"> higher will yield still greater accuracy at the expense of speed.</span>
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<pre style="margin: 0;">+<span id="LC622" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC623" class="line" lang="plaintext">## Version 2.0.0-beta1 - September 22, 2011 ##</span>
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<pre style="margin: 0;">+<span id="LC624" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC625" class="line" lang="plaintext"> * First public release.</span>
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<pre style="margin: 0;">+<span id="LC626" class="line" lang="plaintext"> * Caveats: as of now, the manual is incomplete, there's no tutorial, and no</span>
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<pre style="margin: 0;">+<span id="LC627" class="line" lang="plaintext"> example genome or example reads. All these will be fixed in upcoming</span>
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<pre style="margin: 0;">+<span id="LC628" class="line" lang="plaintext"> releases.</span>
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<pre style="margin: 0;">+<span id="LC629" class="line" lang="plaintext"> * Only a source package is currently available. Platform-specific binaries</span>
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<pre style="margin: 0;">+<span id="LC630" class="line" lang="plaintext"> will be included in future releases.</span></pre>
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<a href="https://salsa.debian.org/med-team/bowtie2/-/commit/cf277464ee949fe563ca814a827b2387be02dbd1#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d"><strong>README.md</strong></a>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="markdown"><span class="c" style="color: #998; font-style: italic;"><!-- badges: start --></span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="markdown"><span class="p">![</span><span class="nv" style="color: #008080;">Github Actions</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/BenLangmead/bowtie2/actions/workflows/bowtie2.yml/badge.svg</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![Generic badge</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/badge/version-2.4.<span class="idiff left right">4</span>-green.svg</span><span class="p">)</span>](https://shields.io/)</span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![Build Status</span><span class="p">](</span><span class="sx" style="color: #d14;">https://travis-ci.org/BenLangmead/bowtie2.svg?branch=master</span><span class="p">)</span>](https://travis-ci.org/BenLangmead/bowtie2)</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="markdown"><span class="c" style="color: #998; font-style: italic;"><span class="idiff left"><!-- </span>[](https://travis-ci.org/BenLangmead/bowtie2)<span class="idiff right"> --></span></span></span>
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<a href="https://salsa.debian.org/med-team/bowtie2/-/commit/cf277464ee949fe563ca814a827b2387be02dbd1#a177c5447e9cdcbfd7d1dc1c7140293d0cfbc779"><strong>aligner_seed.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">@@ -1105,6 +1105,40 @@ SeedAligner::searchSeedBi() {</td>
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1105
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<pre style="margin: 0;"> <span id="LC1105" class="line" lang="cpp"> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">);</span></span>
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1106
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<pre style="margin: 0;"> <span id="LC1106" class="line" lang="cpp"><span class="p">}</span></span>
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1107
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1107
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<pre style="margin: 0;"> <span id="LC1107" class="line" lang="cpp"></span>
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1108
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<pre style="margin: 0;">+<span id="LC1108" class="line" lang="cpp"><span class="kr" style="font-weight: 600;">inline</span> <span class="kt" style="color: #458; font-weight: 600;">void</span></span>
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1109
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<pre style="margin: 0;">+<span id="LC1109" class="line" lang="cpp"><span class="n" style="color: #333;">SeedAligner</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">prefetchNextLocsBi</span><span class="p">(</span></span>
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1110
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<pre style="margin: 0;">+<span id="LC1110" class="line" lang="cpp"> <span class="n" style="color: #333;">TIndexOffU</span> <span class="n" style="color: #333;">topf</span><span class="p">,</span> <span class="c1" style="color: #998; font-style: italic;">// top in BWT</span></span>
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1111
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<pre style="margin: 0;">+<span id="LC1111" class="line" lang="cpp"> <span class="n" style="color: #333;">TIndexOffU</span> <span class="n" style="color: #333;">botf</span><span class="p">,</span> <span class="c1" style="color: #998; font-style: italic;">// bot in BWT</span></span>
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1112
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<pre style="margin: 0;">+<span id="LC1112" class="line" lang="cpp"> <span class="n" style="color: #333;">TIndexOffU</span> <span class="n" style="color: #333;">topb</span><span class="p">,</span> <span class="c1" style="color: #998; font-style: italic;">// top in BWT'</span></span>
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1113
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<pre style="margin: 0;">+<span id="LC1113" class="line" lang="cpp"> <span class="n" style="color: #333;">TIndexOffU</span> <span class="n" style="color: #333;">botb</span><span class="p">,</span> <span class="c1" style="color: #998; font-style: italic;">// bot in BWT'</span></span>
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1114
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<pre style="margin: 0;">+<span id="LC1114" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">step</span> <span class="c1" style="color: #998; font-style: italic;">// step to get ready for</span></span>
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1115
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<pre style="margin: 0;">+<span id="LC1115" class="line" lang="cpp"> <span class="p">)</span></span>
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1116
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<pre style="margin: 0;">+<span id="LC1116" class="line" lang="cpp"><span class="p">{</span></span>
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1117
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<pre style="margin: 0;">+<span id="LC1117" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">step</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)</span><span class="n" style="color: #333;">s_</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">steps</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">())</span> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// no more steps!</span></span>
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1118
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<pre style="margin: 0;">+<span id="LC1118" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Which direction are we going in next?</span></span>
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1119
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<pre style="margin: 0;">+<span id="LC1119" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">s_</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">steps</span><span class="p">[</span><span class="n" style="color: #333;">step</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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1120
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<pre style="margin: 0;">+<span id="LC1120" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Left to right; use BWT'</span></span>
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1121
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<pre style="margin: 0;">+<span id="LC1121" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">botb</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">topb</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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1122
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<pre style="margin: 0;">+<span id="LC1122" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Already down to 1 row; just init top locus</span></span>
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1123
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<pre style="margin: 0;">+<span id="LC1123" class="line" lang="cpp"> <span class="n" style="color: #333;">SideLocus</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">prefetchFromRow</span><span class="p">(</span></span>
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1124
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<pre style="margin: 0;">+<span id="LC1124" class="line" lang="cpp"> <span class="n" style="color: #333;">topb</span><span class="p">,</span> <span class="n" style="color: #333;">ebwtBw_</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">eh</span><span class="p">(),</span> <span class="n" style="color: #333;">ebwtBw_</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">ebwt</span><span class="p">());</span></span>
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1125
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<pre style="margin: 0;">+<span id="LC1125" 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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1126
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<pre style="margin: 0;">+<span id="LC1126" class="line" lang="cpp"> <span class="n" style="color: #333;">SideLocus</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">prefetchFromTopBot</span><span class="p">(</span></span>
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1127
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<pre style="margin: 0;">+<span id="LC1127" class="line" lang="cpp"> <span class="n" style="color: #333;">topb</span><span class="p">,</span> <span class="n" style="color: #333;">botb</span><span class="p">,</span> <span class="n" style="color: #333;">ebwtBw_</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">eh</span><span class="p">(),</span> <span class="n" style="color: #333;">ebwtBw_</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">ebwt</span><span class="p">());</span></span>
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1128
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<pre style="margin: 0;">+<span id="LC1128" class="line" lang="cpp"> <span class="p">}</span></span>
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1129
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<pre style="margin: 0;">+<span id="LC1129" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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1130
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<pre style="margin: 0;">+<span id="LC1130" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Right to left; use BWT</span></span>
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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;">if</span><span class="p">(</span><span class="n" style="color: #333;">botf</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">topf</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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1132
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<pre style="margin: 0;">+<span id="LC1132" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Already down to 1 row; just init top locus</span></span>
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1133
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<pre style="margin: 0;">+<span id="LC1133" class="line" lang="cpp"> <span class="n" style="color: #333;">SideLocus</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">prefetchFromRow</span><span class="p">(</span></span>
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1134
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<pre style="margin: 0;">+<span id="LC1134" class="line" lang="cpp"> <span class="n" style="color: #333;">topf</span><span class="p">,</span> <span class="n" style="color: #333;">ebwtFw_</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">eh</span><span class="p">(),</span> <span class="n" style="color: #333;">ebwtFw_</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">ebwt</span><span class="p">());</span></span>
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1135
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<pre style="margin: 0;">+<span id="LC1135" 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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1136
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<pre style="margin: 0;">+<span id="LC1136" class="line" lang="cpp"> <span class="n" style="color: #333;">SideLocus</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">prefetchFromTopBot</span><span class="p">(</span></span>
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1137
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<pre style="margin: 0;">+<span id="LC1137" class="line" lang="cpp"> <span class="n" style="color: #333;">topf</span><span class="p">,</span> <span class="n" style="color: #333;">botf</span><span class="p">,</span> <span class="n" style="color: #333;">ebwtFw_</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">eh</span><span class="p">(),</span> <span class="n" style="color: #333;">ebwtFw_</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">ebwt</span><span class="p">());</span></span>
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1138
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<pre style="margin: 0;">+<span id="LC1138" class="line" lang="cpp"> <span class="p">}</span></span>
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1139
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<pre style="margin: 0;">+<span id="LC1139" class="line" lang="cpp"> <span class="p">}</span></span>
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1140
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<pre style="margin: 0;">+<span id="LC1140" class="line" lang="cpp"><span class="p">}</span></span>
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1141
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<pre style="margin: 0;">+<span id="LC1141" class="line" lang="cpp"></span>
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1142
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<pre style="margin: 0;"> <span id="LC1142" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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1109
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1143
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<pre style="margin: 0;"> <span id="LC1143" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Get tloc, bloc ready for the next step. If the new range is under</span></span>
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1144
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<pre style="margin: 0;"> <span id="LC1144" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * the ceiling.</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1500" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -1500,6 +1534,8 @@ SeedAligner::searchSeedBi(</td>
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1500
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1534
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<pre style="margin: 0;"> <span id="LC1534" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">ltr</span> <span class="o" style="font-weight: 600;">=</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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1501
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1535
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<pre style="margin: 0;"> <span id="LC1535" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Ebwt</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">ebwt</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ltr</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">ebwtBw_</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">ebwtFw_</span><span class="p">;</span></span>
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1502
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1536
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<pre style="margin: 0;"> <span id="LC1536" class="line" lang="cpp"> <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">ebwt</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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1537
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<pre style="margin: 0;">+<span id="LC1537" 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;">abs</span><span class="p">(</span><span class="n" style="color: #333;">off</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="LC1538" class="line" lang="cpp"> <span class="n" style="color: #333;">__builtin_prefetch</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;">seq_</span><span class="p">)[</span><span class="n" style="color: #333;">off</span><span class="p">]));</span></span>
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1503
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1539
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<pre style="margin: 0;"> <span id="LC1539" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">ltr</span><span class="p">)</span> <span class="p">{</span></span>
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1504
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1540
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<pre style="margin: 0;"> <span id="LC1540" class="line" lang="cpp"> <span class="n" style="color: #333;">tp</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tp</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="n" style="color: #333;">tp</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tp</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">topf</span><span class="p">;</span></span>
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1505
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1541
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<pre style="margin: 0;"> <span id="LC1541" class="line" lang="cpp"> <span class="n" style="color: #333;">bp</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bp</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="n" style="color: #333;">bp</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bp</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">botf</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1521" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1521,13 +1557,16 @@ SeedAligner::searchSeedBi(</td>
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1521
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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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1522
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1558
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<pre style="margin: 0;"> <span id="LC1558" class="line" lang="cpp"> <span class="n" style="color: #333;">TIndexOffU</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">tf</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ltr</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">tp</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">t</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">tb</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ltr</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">t</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">tp</span><span class="p">;</span></span>
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1523
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1559
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<pre style="margin: 0;"> <span id="LC1559" class="line" lang="cpp"> <span class="n" style="color: #333;">TIndexOffU</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">bf</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ltr</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">bp</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">b</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">bb</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ltr</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;">bp</span><span class="p">;</span></span>
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1524
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<pre style="margin: 0;">-<span id="LC1524" 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;">abs</span><span class="p">(</span><span class="n" style="color: #333;">off</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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1560
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<pre style="margin: 0;">+<span id="LC1560" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">seq_</span><span class="p">)[</span><span class="n" style="color: #333;">off</span><span class="p">];</span> <span class="n" style="color: #333;">assert_range</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">4</span><span class="p">,</span> <span class="n" style="color: #333;">c</span><span class="p">);</span></span>
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1561
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<pre style="margin: 0;">+<span id="LC1561" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// not 100% sure we need it, but redundant prefetches are not dangerous</span></span>
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1562
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<pre style="margin: 0;">+<span id="LC1562" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// and helps in the average case</span></span>
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1563
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<pre style="margin: 0;">+<span id="LC1563" class="line" lang="cpp"> <span class="n" style="color: #333;">prefetchNextLocsBi</span><span class="p">(</span><span class="n" style="color: #333;">tf</span><span class="p">[</span><span class="n" style="color: #333;">c</span><span class="p">],</span> <span class="n" style="color: #333;">bf</span><span class="p">[</span><span class="n" style="color: #333;">c</span><span class="p">],</span> <span class="n" style="color: #333;">tb</span><span class="p">[</span><span class="n" style="color: #333;">c</span><span class="p">],</span> <span class="n" style="color: #333;">bb</span><span class="p">[</span><span class="n" style="color: #333;">c</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;">1</span><span class="p">);</span></span>
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1564
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<pre style="margin: 0;">+<span id="LC1564" class="line" lang="cpp"></span>
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1525
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1565
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<pre style="margin: 0;"> <span id="LC1565" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//</span></span>
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1526
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1566
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<pre style="margin: 0;"> <span id="LC1566" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">leaveZone</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">zones</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">first</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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1527
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1567
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<pre style="margin: 0;"> <span id="LC1567" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//bool leaveZoneIns = zones_[i].second < 0;</span></span>
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1528
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1568
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<pre style="margin: 0;"> <span id="LC1568" class="line" lang="cpp"> <span class="n" style="color: #333;">Constraint</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">cons</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">zones</span><span class="p">[</span><span class="n" style="color: #333;">abs</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">zones</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">first</span><span class="p">)];</span></span>
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1529
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1569
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<pre style="margin: 0;"> <span id="LC1569" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//Constraint& insCons = *zones[abs(s.zones[i].second)];</span></span>
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<pre style="margin: 0;">-<span id="LC1530" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">seq_</span><span class="p">)[</span><span class="n" style="color: #333;">off</span><span class="p">];</span> <span class="n" style="color: #333;">assert_range</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">4</span><span class="p">,</span> <span class="n" style="color: #333;">c</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC1570" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">q</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;">qual_</span><span class="p">)[</span><span class="n" style="color: #333;">off</span><span class="p">];</span></span>
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<pre style="margin: 0;"> <span id="LC1571" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Is it legal for us to advance on characters other than 'c'?</span></span>
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1572
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<pre style="margin: 0;"> <span id="LC1572" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="p">(</span><span class="n" style="color: #333;">cons</span><span class="p">.</span><span class="n" style="color: #333;">mustMatch</span><span class="p">()</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">overall</span><span class="p">.</span><span class="n" style="color: #333;">mustMatch</span><span class="p">())</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">4</span><span class="p">)</span> <span class="p">{</span></span>
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<a href="https://salsa.debian.org/med-team/bowtie2/-/commit/cf277464ee949fe563ca814a827b2387be02dbd1#c9b466ab26199558112972a17a75b8c21ac85c19"><strong>aligner_seed.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">@@ -1625,6 +1625,13 @@ protected:</td>
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<pre style="margin: 0;"> <span id="LC1625" class="line" lang="cpp"> <span class="n" style="color: #333;">TIndexOffU</span> <span class="n" style="color: #333;">botb</span><span class="p">,</span> <span class="c1" style="color: #998; font-style: italic;">// bot in BWT'</span></span>
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1626
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<pre style="margin: 0;"> <span id="LC1626" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">step</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// step to get ready for</span></span>
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<pre style="margin: 0;"> <span id="LC1627" class="line" lang="cpp"> </span>
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<pre style="margin: 0;">+<span id="LC1628" class="line" lang="cpp"> <span class="kr" style="font-weight: 600;">inline</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">prefetchNextLocsBi</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC1629" class="line" lang="cpp"> <span class="n" style="color: #333;">TIndexOffU</span> <span class="n" style="color: #333;">topf</span><span class="p">,</span> <span class="c1" style="color: #998; font-style: italic;">// top in BWT</span></span>
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<pre style="margin: 0;">+<span id="LC1630" class="line" lang="cpp"> <span class="n" style="color: #333;">TIndexOffU</span> <span class="n" style="color: #333;">botf</span><span class="p">,</span> <span class="c1" style="color: #998; font-style: italic;">// bot in BWT</span></span>
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<pre style="margin: 0;">+<span id="LC1631" class="line" lang="cpp"> <span class="n" style="color: #333;">TIndexOffU</span> <span class="n" style="color: #333;">topb</span><span class="p">,</span> <span class="c1" style="color: #998; font-style: italic;">// top in BWT'</span></span>
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<pre style="margin: 0;">+<span id="LC1632" class="line" lang="cpp"> <span class="n" style="color: #333;">TIndexOffU</span> <span class="n" style="color: #333;">botb</span><span class="p">,</span> <span class="c1" style="color: #998; font-style: italic;">// bot in BWT'</span></span>
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<pre style="margin: 0;">+<span id="LC1633" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">step</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// step to get ready for</span></span>
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<pre style="margin: 0;">+<span id="LC1634" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC1635" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Following are set in searchAllSeeds then used by searchSeed()</span></span>
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<pre style="margin: 0;"> <span id="LC1636" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// and other protected members.</span></span>
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<pre style="margin: 0;"> <span id="LC1637" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Ebwt</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">ebwtFw_</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// forward index (BWT)</span></span>
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<a href="https://salsa.debian.org/med-team/bowtie2/-/commit/cf277464ee949fe563ca814a827b2387be02dbd1#057e0784d807c7b84958635ddeeb5003f2751ece"><strong>aln_sink.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">@@ -2114,6 +2114,12 @@ void AlnSinkSam::appendMate(</td>
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<pre style="margin: 0;"> <span id="LC2114" 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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2115
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<pre style="margin: 0;"> <span id="LC2115" class="line" lang="cpp"> <span class="n" style="color: #333;">samc_</span><span class="p">.</span><span class="n" style="color: #333;">printComment</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;">name</span><span class="p">);</span></span>
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2116
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2116
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<pre style="margin: 0;"> <span id="LC2116" class="line" lang="cpp"> <span class="n" style="color: #333;">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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2117
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<pre style="margin: 0;">+<span id="LC2117" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">samc_</span><span class="p">.</span><span class="n" style="color: #333;">passthrough</span><span class="p">())</span> <span class="p">{</span></span>
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2118
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<pre style="margin: 0;">+<span id="LC2118" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Original read string</span></span>
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2119
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<pre style="margin: 0;">+<span id="LC2119" class="line" lang="cpp"> <span class="n" style="color: #333;">samc_</span><span class="p">.</span><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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2120
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<pre style="margin: 0;">+<span id="LC2120" 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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2121
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<pre style="margin: 0;">+<span id="LC2121" class="line" lang="cpp"> <span class="p">}</span></span>
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2122
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<pre style="margin: 0;">+<span id="LC2122" class="line" lang="cpp"></span>
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2123
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<pre style="margin: 0;"> <span id="LC2123" class="line" lang="cpp"><span class="p">}</span></span>
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2124
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<pre style="margin: 0;"> <span id="LC2124" class="line" lang="cpp"></span>
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2125
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<pre style="margin: 0;"> <span id="LC2125" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#ifdef ALN_SINK_MAIN</span></span>
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<a href="https://salsa.debian.org/med-team/bowtie2/-/commit/cf277464ee949fe563ca814a827b2387be02dbd1#03d5fe68cb76a542cb9c06b8e03093e21319ca35"><strong>blockwise_sa.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">@@ -22,6 +22,7 @@</td>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="cpp"></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 <stdint.h></span></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <stdlib.h></span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <future></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 <iostream></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 <sstream></span></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <thread></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">@@ -38,6 +39,7 @@</td>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "ds.h"</span></span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "mem_ids.h"</span></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "word_io.h"</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "threadpool.h"</span></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="cpp"><span class="k" style="font-weight: 600;">using</span> <span class="k" style="font-weight: 600;">namespace</span> <span class="n" style="color: #333;">std</span><span class="p">;</span></span>
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45
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="cpp"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="198" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="200" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -198,6 +200,7 @@ public:</td>
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198
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200
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<pre style="margin: 0;"> <span id="LC200" class="line" lang="cpp"> <span class="n" style="color: #333;">KarkkainenBlockwiseSA</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">TStr</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">__text</span><span class="p">,</span></span>
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199
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201
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<pre style="margin: 0;"> <span id="LC201" class="line" lang="cpp"> <span class="n" style="color: #333;">TIndexOffU</span> <span class="n" style="color: #333;">__bucketSz</span><span class="p">,</span></span>
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200
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202
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<pre style="margin: 0;"> <span id="LC202" class="line" lang="cpp"> <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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203
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="cpp"> <span class="n" style="color: #333;">thread_pool</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">pool</span><span class="p">,</span></span>
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201
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204
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<pre style="margin: 0;"> <span id="LC204" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">__dcV</span><span class="p">,</span></span>
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202
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205
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<pre style="margin: 0;"> <span id="LC205" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <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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203
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206
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<pre style="margin: 0;"> <span id="LC206" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">__sanityCheck</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 unfold js-unfold old_line" data-linenumber="208" style="width: 35px; color: rgba(0,0,0,0.3); 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="211" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -208,6 +211,7 @@ public:</td>
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208
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211
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<pre style="margin: 0;"> <span id="LC211" class="line" lang="cpp"> <span class="n" style="color: #333;">InorderBlockwiseSA</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">TStr</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="n" style="color: #333;">__text</span><span class="p">,</span> <span class="n" style="color: #333;">__bucketSz</span><span class="p">,</span> <span class="n" style="color: #333;">__sanityCheck</span><span class="p">,</span> <span class="n" style="color: #333;">__passMemExc</span><span class="p">,</span> <span class="n" style="color: #333;">__verbose</span><span class="p">,</span> <span class="n" style="color: #333;">__logger</span><span class="p">),</span></span>
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209
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<pre style="margin: 0;"> <span id="LC212" class="line" lang="cpp"> <span class="n" style="color: #333;">_sampleSuffs</span><span class="p">(</span><span class="n" style="color: #333;">EBWTB_CAT</span><span class="p">),</span></span>
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213
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<pre style="margin: 0;"> <span id="LC213" class="line" lang="cpp"> <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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214
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="cpp"> <span class="n" style="color: #333;">_pool</span><span class="p">(</span><span class="n" style="color: #333;">pool</span><span class="p">),</span></span>
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211
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215
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<pre style="margin: 0;"> <span id="LC215" class="line" lang="cpp"> <span class="n" style="color: #333;">_itrBucketIdx</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">),</span></span>
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212
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216
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<pre style="margin: 0;"> <span id="LC216" class="line" lang="cpp"> <span class="n" style="color: #333;">_cur</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">),</span></span>
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213
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217
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<pre style="margin: 0;"> <span id="LC217" class="line" lang="cpp"> <span class="n" style="color: #333;">_dcV</span><span class="p">(</span><span class="n" style="color: #333;">__dcV</span><span class="p">),</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="218" style="width: 35px; color: rgba(0,0,0,0.3); 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="222" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -218,17 +222,7 @@ public:</td>
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218
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222
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<pre style="margin: 0;"> <span id="LC222" class="line" lang="cpp"> <span class="n" style="color: #333;">_done</span><span class="p">(</span><span class="nb" style="color: #0086b3;">NULL</span><span class="p">)</span></span>
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219
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223
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<pre style="margin: 0;"> <span id="LC223" class="line" lang="cpp"> <span class="p">{</span> <span class="n" style="color: #333;">_randomSrc</span><span class="p">.</span><span class="n" style="color: #333;">init</span><span class="p">(</span><span class="n" style="color: #333;">__seed</span><span class="p">);</span> <span class="n" style="color: #333;">reset</span><span class="p">();</span> <span class="p">}</span></span>
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220
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224
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<pre style="margin: 0;"> <span id="LC224" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC221" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">~</span><span class="n" style="color: #333;">KarkkainenBlockwiseSA</span><span class="p">()</span> <span class="k" style="font-weight: 600;">throw</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC222" class="line" lang="cpp"> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC223" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">_threads</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC224" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">tid</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;">tid</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">_threads</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="n" style="color: #333;">tid</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC225" class="line" lang="cpp"> <span class="n" style="color: #333;">_threads</span><span class="p">[</span><span class="n" style="color: #333;">tid</span><span class="p">]</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">join</span><span class="p">();</span></span>
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<pre style="margin: 0;">-<span id="LC226" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">delete</span> <span class="n" style="color: #333;">_threads</span><span class="p">[</span><span class="n" style="color: #333;">tid</span><span class="p">];</span></span>
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<pre style="margin: 0;">-<span id="LC227" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC228" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC229" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">_done</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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<pre style="margin: 0;">-<span id="LC230" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">delete</span><span class="p">[]</span> <span class="n" style="color: #333;">_done</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC231" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">~</span><span class="n" style="color: #333;">KarkkainenBlockwiseSA</span><span class="p">()</span> <span class="k" style="font-weight: 600;">throw</span><span class="p">()</span> <span class="p">{}</span></span>
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<pre style="margin: 0;"> <span id="LC226" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC227" 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="LC228" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Allocate an amount of memory that simulates the peak memory</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">@@ -253,7 +247,7 @@ public:</td>
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<pre style="margin: 0;"> <span id="LC247" class="line" lang="cpp"> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC248" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Launch threads if not</span></span>
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<pre style="margin: 0;"> <span id="LC249" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_nthreads</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC256" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">_t<span class="idiff left right">hread</span>s</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC250" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">_t<span class="idiff left right">param</span>s</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC251" class="line" lang="cpp"> <span class="n" style="color: #333;">_done</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="k" style="font-weight: 600;">volatile</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span><span class="p">[</span><span class="n" style="color: #333;">_sampleSuffs</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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252
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<pre style="margin: 0;"> <span id="LC252" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">_sampleSuffs</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="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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259
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253
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<pre style="margin: 0;"> <span id="LC253" class="line" lang="cpp"> <span class="n" style="color: #333;">_done</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="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="257" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -263,9 +257,11 @@ public:</td>
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263
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257
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<pre style="margin: 0;"> <span id="LC257" 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;">tid</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;">tid</span> <span class="o" style="font-weight: 600;"><</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_nthreads</span><span class="p">;</span> <span class="n" style="color: #333;">tid</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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264
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258
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<pre style="margin: 0;"> <span id="LC258" class="line" lang="cpp"> <span class="n" style="color: #333;">_tparams</span><span class="p">[</span><span class="n" style="color: #333;">tid</span><span class="p">].</span><span class="n" style="color: #333;">first</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">this</span><span class="p">;</span></span>
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265
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259
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<pre style="margin: 0;"> <span id="LC259" class="line" lang="cpp"> <span class="n" style="color: #333;">_tparams</span><span class="p">[</span><span class="n" style="color: #333;">tid</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;">tid</span><span class="p">;</span></span>
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266
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<pre style="margin: 0;">-<span id="LC266" class="line" lang="cpp"> <span class="n" style="color: #333;">_threads</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="k" style="font-weight: 600;">new</span> <span class="kr" style="font-weight: 600;">thread</span><span class="p">(</span><span class="n" style="color: #333;">nextBlock_Worker</span><span class="p">((</span><span class="kt" style="color: #458; font-weight: 600;">void</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;">_tparams</span><span class="p">[</span><span class="n" style="color: #333;">tid</span><span class="p">])));</span></span>
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260
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<pre style="margin: 0;">+<span id="LC260" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">tid</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">_nthreads</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="261" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
261
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<pre style="margin: 0;">+<span id="LC261" class="line" lang="cpp"> <span class="n" style="color: #333;">nextBlock_Worker</span><span class="p">((</span><span class="kt" style="color: #458; font-weight: 600;">void</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;">_tparams</span><span class="p">[</span><span class="n" style="color: #333;">tid</span><span class="p">]);</span></span>
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262
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<pre style="margin: 0;">+<span id="LC262" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span></span>
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263
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<pre style="margin: 0;">+<span id="LC263" class="line" lang="cpp"> <span class="n" style="color: #333;">_pool</span><span class="p">.</span><span class="n" style="color: #333;">submit</span><span class="p">(</span><span class="n" style="color: #333;">nextBlock_Worker</span><span class="p">((</span><span class="kt" style="color: #458; font-weight: 600;">void</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;">_tparams</span><span class="p">[</span><span class="n" style="color: #333;">tid</span><span class="p">]));</span></span>
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267
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264
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<pre style="margin: 0;"> <span id="LC264" class="line" lang="cpp"> <span class="p">}</span></span>
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268
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<pre style="margin: 0;">-<span id="LC268" class="line" lang="cpp"> <span class="n" style="color: #333;">assert_eq</span><span class="p">(</span><span class="n" style="color: #333;">_threads</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">(),</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span><span class="p">)</span><span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_nthreads</span><span class="p">);</span></span>
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269
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265
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<pre style="margin: 0;"> <span id="LC265" class="line" lang="cpp"> <span class="p">}</span></span>
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270
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266
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<pre style="margin: 0;"> <span id="LC266" class="line" lang="cpp"> <span class="p">}</span></span>
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271
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267
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<pre style="margin: 0;"> <span id="LC267" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_itrPushedBackSuffix</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">OFF_MASK</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="396" style="width: 35px; color: rgba(0,0,0,0.3); 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="392" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -396,7 +392,7 @@ private:</td>
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396
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392
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<pre style="margin: 0;"> <span id="LC392" class="line" lang="cpp"> <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">_dc</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">()</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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397
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393
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<pre style="margin: 0;"> <span id="LC393" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">_dcV</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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398
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394
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<pre style="margin: 0;"> <span id="LC394" class="line" lang="cpp"> <span class="n" style="color: #333;">_dc</span><span class="p">.</span><span class="n" style="color: #333;">init</span><span class="p">(</span><span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">TDC</span><span class="p">(</span><span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">text</span><span class="p">(),</span> <span class="n" style="color: #333;">_dcV</span><span class="p">,</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">verbose</span><span class="p">(),</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">sanityCheck</span><span class="p">()));</span></span>
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<pre style="margin: 0;">-<span id="LC399" class="line" lang="cpp"> <span class="n" style="color: #333;">_dc</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">()</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">build</span><span class="p">(</span><span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_nthreads</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC395" class="line" lang="cpp"> <span class="n" style="color: #333;">_dc</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">()</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">build</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">_pool</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_nthreads</span><span class="p">);</span></span>
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396
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<pre style="margin: 0;"> <span id="LC396" class="line" lang="cpp"> <span class="p">}</span></span>
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397
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<pre style="margin: 0;"> <span id="LC397" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Calculate sample suffixes</span></span>
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402
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398
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<pre style="margin: 0;"> <span id="LC398" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">bucketSz</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><=</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">text</span><span class="p">().</span><span class="n" style="color: #333;">length</span><span class="p">())</span> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="432" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -436,6 +432,7 @@ private:</td>
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<pre style="margin: 0;"> <span id="LC432" class="line" lang="cpp"></span>
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437
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433
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<pre style="margin: 0;"> <span id="LC433" class="line" lang="cpp"> <span class="n" style="color: #333;">EList</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="n" style="color: #333;">_sampleSuffs</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">/// sample suffixes</span></span>
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438
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<pre style="margin: 0;"> <span id="LC434" class="line" lang="cpp"> <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;">/// # of threads</span></span>
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<pre style="margin: 0;">+<span id="LC435" class="line" lang="cpp"> <span class="n" style="color: #333;">thread_pool</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">_pool</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC436" class="line" lang="cpp"> <span class="n" style="color: #333;">TIndexOffU</span> <span class="n" style="color: #333;">_itrBucketIdx</span><span class="p">;</span></span>
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440
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<pre style="margin: 0;"> <span id="LC437" class="line" lang="cpp"> <span class="n" style="color: #333;">TIndexOffU</span> <span class="n" style="color: #333;">_cur</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">/// offset to 1st elt of next block</span></span>
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<pre style="margin: 0;"> <span id="LC438" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">_dcV</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">/// difference-cover periodicity</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">@@ -522,7 +519,7 @@ struct BinarySortingParam {</td>
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<pre style="margin: 0;"> <span id="LC519" class="line" lang="cpp"><span class="p">};</span></span>
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<pre style="margin: 0;"> <span id="LC520" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC521" class="line" lang="cpp"><span class="k" style="font-weight: 600;">template</span><span class="o" style="font-weight: 600;"><</span><span class="k" style="font-weight: 600;">typename</span> <span class="nc" style="color: #458; font-weight: 600;">TStr</span><span class="p">></span></span>
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<pre style="margin: 0;">-<span id="LC525" class="line" lang="cpp"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">BinarySorting_worker</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC522" class="line" lang="cpp"><span class="k" style="font-weight: 600;">class</span> <span class="idiff left right"> </span><span class="nc" style="color: #458; font-weight: 600;">BinarySorting_worker</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC523" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">vp</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC524" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC525" class="line" lang="cpp"><span class="nl">public:</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">@@ -638,7 +635,7 @@ void KarkkainenBlockwiseSA<TStr>::buildSamples() {</td>
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<pre style="margin: 0;"> <span id="LC635" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Iterate until all buckets are less than</span></span>
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<pre style="margin: 0;"> <span id="LC636" class="line" lang="cpp"> <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;">limit</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="LC637" class="line" lang="cpp"> <span class="n" style="color: #333;">TIndexOffU</span> <span class="n" style="color: #333;">numBuckets</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">TIndexOffU</span><span class="p">)</span><span class="n" style="color: #333;">_sampleSuffs</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="LC641" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">AutoArray</span></span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="n" style="color: #333;"><span class="idiff">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="kr" style="font-weight: 600;"><span class="idiff">thread</span></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">threads</span></span><span class="p"><span class="idiff">(</span></span><span class="k" style="font-weight: 600;"><span class="idiff">this</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff right">_nthreads</span></span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC638" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">vector</span></span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="n" style="color: #333;"><span class="idiff">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">future</span></span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">void</span></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="n" style="color: #333;"><span class="idiff">threads</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">_pool</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">size</span></span><span class="p"><span class="idiff right">()</span>);</span></span>
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<pre style="margin: 0;"> <span id="LC639" 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;">BinarySortingParam</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">TStr</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">tparams</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC640" class="line" lang="cpp"> <span class="n" style="color: #333;">tparams</span><span class="p">.</span><span class="n" style="color: #333;">resize</span><span class="p">(</span><span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_nthreads</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC641" 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;">tid</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;">tid</span> <span class="o" style="font-weight: 600;"><</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_nthreads</span><span class="p">;</span> <span class="n" style="color: #333;">tid</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -665,19 +662,17 @@ void KarkkainenBlockwiseSA<TStr>::buildSamples() {</td>
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<pre style="margin: 0;"> <span id="LC662" class="line" lang="cpp"> <span class="n" style="color: #333;">tparams</span><span class="p">[</span><span class="n" style="color: #333;">tid</span><span class="p">].</span><span class="n" style="color: #333;">sampleSuffs</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">_sampleSuffs</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC663" class="line" lang="cpp"> <span class="n" style="color: #333;">tparams</span><span class="p">[</span><span class="n" style="color: #333;">tid</span><span class="p">].</span><span class="n" style="color: #333;">begin</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">tid</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">?</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">/</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_nthreads</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">tid</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC664" class="line" lang="cpp"> <span class="n" style="color: #333;">tparams</span><span class="p">[</span><span class="n" style="color: #333;">tid</span><span class="p">].</span><span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">tid</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="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_nthreads</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">/</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_nthreads</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="n" style="color: #333;">tid</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="LC668" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_nthreads</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC665" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_nthreads</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;"><span class="idiff left">1</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">tid</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">_nthreads</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="idiff right"> </span><span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC666" class="line" lang="cpp"> <span class="n" style="color: #333;">BinarySorting_worker</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">TStr</span><span class="o" style="font-weight: 600;">></span><span class="p">((</span><span class="kt" style="color: #458; font-weight: 600;">void</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;">tparams</span><span class="p">[</span><span class="n" style="color: #333;">tid</span><span class="p">])();</span></span>
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<pre style="margin: 0;"> <span id="LC667" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC671" class="line" lang="cpp"> <span class="n" style="color: #333;">threads</span><span class="p">[</span><span class="n" style="color: #333;">tid</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;"><span class="idiff left">new</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="kr" style="font-weight: 600;"><span class="idiff right">thread</span></span><span class="p">(</span><span class="n" style="color: #333;">BinarySorting_worker</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">TStr</span><span class="o" style="font-weight: 600;">></span><span class="p">(((</span><span class="kt" style="color: #458; font-weight: 600;">void</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;">tparams</span><span class="p">[</span><span class="n" style="color: #333;">tid</span><span class="p">])));</span></span>
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<pre style="margin: 0;">+<span id="LC668" class="line" lang="cpp"> <span class="n" style="color: #333;">threads</span><span class="p">[</span><span class="n" style="color: #333;">tid</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">_pool</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">submit</span></span><span class="p">(</span><span class="n" style="color: #333;">BinarySorting_worker</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">TStr</span><span class="o" style="font-weight: 600;">></span><span class="p">(((</span><span class="kt" style="color: #458; font-weight: 600;">void</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;">tparams</span><span class="p">[</span><span class="n" style="color: #333;">tid</span><span class="p">])));</span></span>
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<pre style="margin: 0;"> <span id="LC669" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC670" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC671" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC672" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_nthreads</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC676" 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;">tid</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;">tid</span> <span class="o" style="font-weight: 600;"><</span> <span class="k" style="font-weight: 600;"><span class="idiff left">this</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff right">_nthreads</span></span><span class="p">;</span> <span class="n" style="color: #333;">tid</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC677" class="line" lang="cpp"> <span class="n" style="color: #333;">threads</span><span class="p">[</span><span class="n" style="color: #333;">tid</span><span class="p">]</span><span class="o" style="font-weight: 600;"><span class="idiff left">-></span></span><span class="n" style="color: #333;"><span class="idiff right">join</span></span><span class="p">();</span></span>
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<pre style="margin: 0;">+<span id="LC673" 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;">tid</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;">tid</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;"><span class="idiff left">_pool</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">size</span></span><span class="p"><span class="idiff right">()</span>;</span> <span class="n" style="color: #333;">tid</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC674" class="line" lang="cpp"> <span class="n" style="color: #333;">threads</span><span class="p">[</span><span class="n" style="color: #333;">tid</span><span class="p">]<span class="idiff left">.</span></span><span class="n" style="color: #333;"><span class="idiff right">get</span></span><span class="p">();</span></span>
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<pre style="margin: 0;"> <span id="LC675" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC679" 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;">tid</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;">tid</span> <span class="o" style="font-weight: 600;"><</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_nthreads</span><span class="p">;</span> <span class="n" style="color: #333;">tid</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC680" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">delete</span> <span class="n" style="color: #333;">threads</span><span class="p">[</span><span class="n" style="color: #333;">tid</span><span class="p">];</span></span>
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<pre style="margin: 0;"> <span id="LC676" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC677" 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;">TIndexOffU</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">bucketSzs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tparams</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">bucketSzs</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC678" 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;">TIndexOffU</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">bucketReps</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tparams</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">bucketReps</span><span class="p">;</span></span>
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<a href="https://salsa.debian.org/med-team/bowtie2/-/commit/cf277464ee949fe563ca814a827b2387be02dbd1#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">@@ -19,14 +19,24 @@</td>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="python"><span class="s" style="color: #d14;"> along with Bowtie 2. If not, see <http://www.gnu.org/licenses/>.</span></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="python"><span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">os</span></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">sys</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">gzip</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">struct</span></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">inspect</span></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">logging</span></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">argparse</span></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">subprocess</span></span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">collections</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">deque</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">get_gunzip_size</span><span class="p">(</span><span class="n" style="color: #333;">fn</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="python"> <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>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">gzip</span><span class="p">.</span><span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">fn</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">f</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="python"> <span class="k" style="font-weight: 600;">while</span> <span class="bp" style="color: #999;">True</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="python"> <span class="n" style="color: #333;">data</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">f</span><span class="p">.</span><span class="n" style="color: #333;">read</span><span class="p">(</span><span class="mi" style="color: #099;">8192</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="python"> <span class="n" style="color: #333;">size</span> <span class="o" style="font-weight: 600;">+=</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">data</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="python"> <span class="k" style="font-weight: 600;">break</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">size</span></span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">main</span><span class="p">():</span></span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="python"> <span class="n" style="color: #333;">parser</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">argparse</span><span class="p">.</span><span class="n" style="color: #333;">ArgumentParser</span><span class="p">(</span><span class="n" style="color: #333;">add_help</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">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">@@ -51,11 +61,6 @@ def main():</td>
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="python"> <span class="n" style="color: #333;">build_bin_spec</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">ex_path</span><span class="p">,</span><span class="n" style="color: #333;">build_bin_s</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="python"> <span class="n" style="color: #333;">script_options</span><span class="p">,</span> <span class="n" style="color: #333;">argv</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">parse_known_args</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="python"> <span class="n" style="color: #333;">print_help</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>
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<pre style="margin: 0;">-<span id="LC55" 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;">deque</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="LC56" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">'-h'</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">argv</span> <span class="ow" style="font-weight: 600;">or</span> <span class="s" style="color: #d14;">'--help'</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">argv</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="python"> <span class="n" style="color: #333;">print_help</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span></span>
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">script_options</span><span class="p">.</span><span class="n" style="color: #333;">verbose</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="python"> <span class="n" style="color: #333;">logging</span><span class="p">.</span><span class="n" style="color: #333;">getLogger</span><span class="p">().</span><span class="n" style="color: #333;">setLevel</span><span class="p">(</span><span class="n" style="color: #333;">logging</span><span class="p">.</span><span class="n" style="color: #333;">INFO</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">@@ -68,23 +73,41 @@ def main():</td>
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="python"> <span class="n" style="color: #333;">build_bin_spec</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">'-sanitized'</span></span>
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="python"> <span class="n" style="color: #333;">build_bin_l</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">'-sanitized'</span></span>
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="python"> <span class="n" style="color: #333;">fastas</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">'-c'</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">argv</span> <span class="ow" style="font-weight: 600;">and</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">argv</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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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">index</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">reversed</span><span class="p">(</span><span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">argv</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="LC79" class="line" lang="python"> <span class="n" style="color: #333;">arg</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="n" style="color: #333;">index</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">arg</span><span class="p">.</span><span class="n" style="color: #333;">startswith</span><span class="p">(</span><span class="s" style="color: #d14;">'-'</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">arg</span><span class="p">.</span><span class="n" style="color: #333;">isdigit</span><span class="p">():</span></span>
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="python"> <span class="k" style="font-weight: 600;">break</span></span>
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="python"> <span class="n" style="color: #333;">fastas</span><span class="p">.</span><span class="n" style="color: #333;">insert</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">arg</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;">argv</span><span class="p">.</span><span class="n" style="color: #333;">remove</span><span class="p">(</span><span class="n" style="color: #333;">arg</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">fastas</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="python"> <span class="n" style="color: #333;">fastas</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">','</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">fastas</span><span class="p">)</span></span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="python"> <span class="n" style="color: #333;">argv</span><span class="p">.</span><span class="n" style="color: #333;">insert</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">argv</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">fastas</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="python"></span>
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71
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88
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">script_options</span><span class="p">.</span><span class="n" style="color: #333;">large_index</span><span class="p">:</span></span>
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89
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<pre style="margin: 0;"> <span id="LC89" class="line" lang="python"> <span class="n" style="color: #333;">build_bin_spec</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">ex_path</span><span class="p">,</span><span class="n" style="color: #333;">build_bin_l</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC73" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">argv</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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<pre style="margin: 0;">-<span id="LC74" class="line" lang="python"> <span class="n" style="color: #333;">ref_fnames</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">argv</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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<pre style="margin: 0;">+<span id="LC90" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">fastas</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="python"> <span class="n" style="color: #333;">tot_size</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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<pre style="margin: 0;">-<span id="LC76" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">fn</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;"><span class="idiff left right">ref_fname</span>s</span><span class="p">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">','</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">fn</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;"><span class="idiff left right">fasta</span>s</span><span class="p">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">','</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC93" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">exists</span><span class="p">(</span><span class="n" style="color: #333;">fn</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;">statinfo</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">stat</span><span class="p">(</span><span class="n" style="color: #333;">fn</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;">tot_size</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">statinfo</span><span class="p">.</span><span class="n" style="color: #333;">st_size</span></span>
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">fn</span><span class="p">.</span><span class="n" style="color: #333;">endswith</span><span class="p">(</span><span class="s" style="color: #d14;">'.gz'</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">fn</span><span class="p">.</span><span class="n" style="color: #333;">endswith</span><span class="p">(</span><span class="s" style="color: #d14;">".Z"</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="python"> <span class="n" style="color: #333;">tot_size</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">get_gunzip_size</span><span class="p">(</span><span class="n" style="color: #333;">fn</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="python"> <span class="n" style="color: #333;">statinfo</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">stat</span><span class="p">(</span><span class="n" style="color: #333;">fn</span><span class="p">)</span></span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="python"> <span class="n" style="color: #333;">tot_size</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">statinfo</span><span class="p">.</span><span class="n" style="color: #333;">st_size</span></span>
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99
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">tot_size</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">small_index_max_size</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="python"> <span class="n" style="color: #333;">build_bin_spec</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">ex_path</span><span class="p">,</span><span class="n" style="color: #333;">build_bin_l</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="python"></span>
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<pre style="margin: 0;">-<span id="LC83" class="line" lang="python"> <span class="n" style="color: #333;">argv</span><span class="p">.</span><span class="n" style="color: #333;">appendleft</span><span class="p">(</span><span class="s" style="color: #d14;">'basic-0'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC84" class="line" lang="python"> <span class="n" style="color: #333;">argv</span><span class="p">.</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="LC85" class="line" lang="python"> <span class="n" style="color: #333;">argv</span><span class="p">.</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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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">exists</span><span class="p">(</span><span class="n" style="color: #333;">build_bin_spec</span><span class="p">):</span></span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">stderr</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">'{0} does not exist, try running `[g]make {0}</span><span class="se" style="color: #d14;">\'\n</span><span class="s" style="color: #d14;">'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">basename</span><span class="p">(</span><span class="n" style="color: #333;">build_bin_spec</span><span class="p">)))</span></span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="nb" style="color: #0086b3;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="python"></span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="python"> <span class="n" style="color: #333;">argv</span><span class="p">.</span><span class="n" style="color: #333;">insert</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="s" style="color: #d14;">'basic-0'</span><span class="p">)</span></span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="python"> <span class="n" style="color: #333;">argv</span><span class="p">.</span><span class="n" style="color: #333;">insert</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="s" style="color: #d14;">'--wrapper'</span><span class="p">)</span></span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="python"> <span class="n" style="color: #333;">argv</span><span class="p">.</span><span class="n" style="color: #333;">insert</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">build_bin_spec</span><span class="p">)</span></span>
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109
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<pre style="margin: 0;"> <span id="LC109" class="line" lang="python"> <span class="n" style="color: #333;">logging</span><span class="p">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">'Command: %s'</span> <span class="o" style="font-weight: 600;">%</span> <span class="s" style="color: #d14;">' '</span><span class="p">.</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="LC87" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="nb" style="color: #0086b3;">exit</span><span class="p">(</span><span class="n" style="color: #333;">subprocess</span><span class="p">.</span><span class="n" style="color: #333;">call</span><span class="p">(</span><span class="nb" style="color: #0086b3;"><span class="idiff left">list</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;">argv</span><span class="p">))<span class="idiff right">)</span></span></span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="nb" style="color: #0086b3;">exit</span><span class="p">(</span><span class="n" style="color: #333;">subprocess</span><span class="p">.</span><span class="n" style="color: #333;">call</span><span class="p">(</span><span class="n" style="color: #333;">argv</span><span class="p">))</span></span>
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111
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<pre style="margin: 0;"> <span id="LC111" class="line" lang="python"></span>
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112
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<pre style="margin: 0;"> <span id="LC112" 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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113
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<pre style="margin: 0;"> <span id="LC113" 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/cf277464ee949fe563ca814a827b2387be02dbd1#999fd61d6ccb4c3bc242370d11e9095438b9e1d1"><strong>bt2_build.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">@@ -138,17 +138,17 @@ static void printUsage(ostream& out) {</td>
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138
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138
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<pre style="margin: 0;"> <span id="LC138" class="line" lang="cpp"> <span class="n" style="color: #333;">out</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Usage: "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">tool_name</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" [options]* <reference_in> <bt2_index_base>"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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139
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139
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<pre style="margin: 0;"> <span id="LC139" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" reference_in comma-separated list of files with ref sequences"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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140
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140
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<pre style="margin: 0;"> <span id="LC140" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" bt2_index_base write "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">gEbwt_ext</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">" data to files with this dir/basename"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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141
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<pre style="margin: 0;">-<span id="LC141" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"*** Bowtie 2 indexes w<span class="idiff left right">ork only with v2 (not v1). Likewise for v1 indexes</span>. ***"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"*** Bowtie 2 indexes w<span class="idiff left right">ill work with Bowtie v1.2.3 and later</span>. ***"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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142
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142
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<pre style="margin: 0;"> <span id="LC142" 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>
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143
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143
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<pre style="margin: 0;"> <span id="LC143" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" -f reference files are Fasta (default)"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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144
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144
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<pre style="margin: 0;"> <span id="LC144" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" -c reference sequences given on cmd line (as"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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145
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145
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<pre style="margin: 0;"> <span id="LC145" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" <reference_in>)"</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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146
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146
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<pre style="margin: 0;"> <span id="LC146" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">wrapper</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"basic-0"</span><span class="p">)</span> <span class="p">{</span></span>
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147
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147
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<pre style="margin: 0;"> <span id="LC147" class="line" lang="cpp"> <span class="n" style="color: #333;">out</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" --large-index force generated index to be 'large', even if ref"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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148
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<pre style="margin: 0;">-<span id="LC148" class="line" lang="cpp"> <span class="idiff left right"> </span><span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" has fewer than 4 billion nucleotides"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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149
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<pre style="margin: 0;">-<span id="LC149" class="line" lang="cpp"> <span class="idiff left right"> </span><span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" --debug use the debug binary; slower, assertions enabled"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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150
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<pre style="margin: 0;">-<span id="LC150" class="line" lang="cpp"> <span class="idiff left right"> </span><span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" --sanitized use sanitized binary; slower, uses ASan and/or UBSan"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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151
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<pre style="margin: 0;">-<span id="LC151" class="line" lang="cpp"> <span class="idiff left right"> </span><span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" --verbose log the issued command"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="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="cpp"> <span class="idiff left right"> </span><span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" has fewer than 4 billion nucleotides"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="cpp"> <span class="idiff left right"> </span><span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" --debug use the debug binary; slower, assertions enabled"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="cpp"> <span class="idiff left right"> </span><span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" --sanitized use sanitized binary; slower, uses ASan and/or UBSan"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="cpp"> <span class="idiff left right"> </span><span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" --verbose log the issued command"</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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152
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152
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<pre style="margin: 0;"> <span id="LC152" class="line" lang="cpp"> <span class="p">}</span></span>
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153
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153
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<pre style="margin: 0;"> <span id="LC153" class="line" lang="cpp"> <span class="n" style="color: #333;">out</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" -a/--noauto disable automatic -p/--bmax/--dcv memory-fitting"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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154
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154
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<pre style="margin: 0;"> <span id="LC154" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" -p/--packed use packed strings internally; slower, less memory"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="166" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -166,16 +166,15 @@ static void printUsage(ostream& out) {</td>
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166
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166
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<pre style="margin: 0;"> <span id="LC166" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//<< (currentlyBigEndian()? "big":"little") << ")" << endl</span></span>
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167
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167
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<pre style="margin: 0;"> <span id="LC167" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" --seed <int> seed for random number generator"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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168
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168
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<pre style="margin: 0;"> <span id="LC168" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" -q/--quiet verbose output (for debugging)"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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169
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<pre style="margin: 0;">-<span id="LC169" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" -h/--help print detailed description of tool and its options"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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170
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<pre style="margin: 0;">-<span id="LC170" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" --usage print this usage message"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" --h/--help print this message and quit"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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171
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170
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<pre style="margin: 0;"> <span id="LC170" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" --version print version information and quit"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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172
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171
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<pre style="margin: 0;"> <span id="LC171" class="line" lang="cpp"> <span class="p">;</span></span>
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173
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172
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<pre style="margin: 0;"> <span id="LC172" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">wrapper</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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174
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173
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<pre style="margin: 0;"> <span id="LC173" class="line" lang="cpp"> <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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175
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174
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<pre style="margin: 0;"> <span id="LC174" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"*** Warning ***"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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176
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<pre style="margin: 0;">-<span id="LC176" class="line" lang="cpp"> <span class="idiff left right"> </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;">tool_name</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"' was run directly. It is recommended "</span></span>
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177
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<pre style="margin: 0;">-<span id="LC177" class="line" lang="cpp"> <span class="idiff left right"> </span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"that you run the wrapper script 'bowtie2-build' instead."</span></span>
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178
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<pre style="margin: 0;">-<span id="LC178" class="line" lang="cpp"> <span class="idiff left right"> </span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="cpp"> <span class="idiff left right"> </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;">tool_name</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"' was run directly. It is recommended "</span></span>
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<td class="new_line diff-line-num new" data-linenumber="176" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="cpp"> <span class="idiff left right"> </span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"that you run the wrapper script 'bowtie2-build' instead."</span></span>
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177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="cpp"> <span class="idiff left right"> </span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC178" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC179" class="line" lang="cpp"><span class="p">}</span></span>
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180
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<pre style="margin: 0;"> <span id="LC180" class="line" lang="cpp"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -360,6 +359,14 @@ static void deleteIdxFiles(</td>
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359
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<pre style="margin: 0;"> <span id="LC359" class="line" lang="cpp"> <span class="p">}</span></span>
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361
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360
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<pre style="margin: 0;"> <span id="LC360" class="line" lang="cpp"><span class="p">}</span></span>
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362
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361
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<pre style="margin: 0;"> <span id="LC361" class="line" lang="cpp"></span>
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362
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<pre style="margin: 0;">+<span id="LC362" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">renameIdxFiles</span><span class="p">()</span> <span class="p">{</span></span>
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363
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<pre style="margin: 0;">+<span id="LC363" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">filesWritten</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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364
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<pre style="margin: 0;">+<span id="LC364" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">oldName</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">filesWritten</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">".tmp"</span><span class="p">;</span></span>
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365
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<pre style="margin: 0;">+<span id="LC365" class="line" lang="cpp"> <span class="n" style="color: #333;">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;">"Renaming "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">oldName</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" to "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">filesWritten</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;">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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366
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<pre style="margin: 0;">+<span id="LC366" 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;">rename</span><span class="p">(</span><span class="n" style="color: #333;">oldName</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">(),</span> <span class="n" style="color: #333;">filesWritten</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">c_str</span><span class="p">());</span></span>
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367
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<pre style="margin: 0;">+<span id="LC367" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC368" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC369" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC370" 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="LC371" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Drive the index construction process and optionally sanity-check the</span></span>
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<pre style="margin: 0;"> <span id="LC372" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * result.</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">@@ -686,7 +693,6 @@ int bowtie_build(int argc, const char **argv) {</td>
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686
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693
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<pre style="margin: 0;"> <span id="LC693" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">packed</span><span class="p">)</span> <span class="p">{</span></span>
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687
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694
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<pre style="margin: 0;"> <span id="LC694" class="line" lang="cpp"> <span class="n" style="color: #333;">driver</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">S2bDnaString</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="n" style="color: #333;">infile</span><span class="p">,</span> <span class="n" style="color: #333;">infiles</span><span class="p">,</span> <span class="n" style="color: #333;">outfile</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">".rev"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">,</span> <span class="n" style="color: #333;">reverseType</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC695" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC689" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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696
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<pre style="margin: 0;"> <span id="LC696" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">catch</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">exception</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">e</span><span class="p">)</span> <span class="p">{</span></span>
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691
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697
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<pre style="margin: 0;"> <span id="LC697" 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: Encountered exception: '"</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="s" style="color: #d14;">"'"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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692
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698
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<pre style="margin: 0;"> <span id="LC698" 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;">"Command: "</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">@@ -704,5 +710,7 @@ int bowtie_build(int argc, const char **argv) {</td>
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704
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710
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<pre style="margin: 0;"> <span id="LC710" class="line" lang="cpp"> <span class="n" style="color: #333;">deleteIdxFiles</span><span class="p">(</span><span class="n" style="color: #333;">outfile</span><span class="p">,</span> <span class="n" style="color: #333;">writeRef</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">justRef</span><span class="p">,</span> <span class="n" style="color: #333;">justRef</span><span class="p">);</span></span>
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705
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711
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<pre style="margin: 0;"> <span id="LC711" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">e</span><span class="p">;</span></span>
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712
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<pre style="margin: 0;"> <span id="LC712" class="line" lang="cpp"> <span class="p">}</span></span>
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713
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<pre style="margin: 0;">+<span id="LC713" class="line" lang="cpp"> <span class="n" style="color: #333;">renameIdxFiles</span><span class="p">();</span></span>
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714
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<pre style="margin: 0;">+<span id="LC714" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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715
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<pre style="margin: 0;"> <span id="LC715" class="line" lang="cpp"><span class="p">}</span></span>
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716
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<pre style="margin: 0;"> <span id="LC716" class="line" lang="cpp"><span class="p">}</span></span></pre>
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<li id="d1904db8401bf0137951f60c3d4a34a7cf8e2e84">
<a href="https://salsa.debian.org/med-team/bowtie2/-/commit/cf277464ee949fe563ca814a827b2387be02dbd1#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">@@ -54,6 +54,7 @@</td>
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54
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54
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "random_source.h"</span></span>
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55
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55
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "mem_ids.h"</span></span>
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56
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56
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "btypes.h"</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "threadpool.h"</span></span>
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58
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="cpp"></span>
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59
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#ifdef POPCNT_CAPABILITY</span></span>
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60
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "processor_support.h"</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">@@ -327,43 +328,93 @@ struct SideLocus {</td>
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327
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328
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<pre style="margin: 0;"> <span id="LC328" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">EbwtParams</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">ep</span><span class="p">,</span></span>
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328
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329
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<pre style="margin: 0;"> <span id="LC329" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uint8_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">ebwt</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC330" class="line" lang="cpp"> <span class="n" style="color: #333;">SideLocus</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">ltop</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC330" class="line" lang="cpp"> <span class="n" style="color: #333;">SideLocus</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">lbot</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC331" class="line" lang="cpp"> <span class="n" style="color: #333;">SideLocus</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">lbot</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC332" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">prefetch</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="LC333" class="line" lang="cpp"> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC334" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">TIndexOffU</span> <span class="n" style="color: #333;">sideBwtLen</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ep</span><span class="p">.</span><span class="n" style="color: #333;">_sideBwtLen</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC335" class="line" lang="cpp"> <span class="n" style="color: #333;">assert_gt</span><span class="p">(</span><span class="n" style="color: #333;">bot</span><span class="p">,</span> <span class="n" style="color: #333;">top</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC334" class="line" lang="cpp"> <span class="n" style="color: #333;">ltop</span><span class="p">.</span><span class="n" style="color: #333;">initFromRow</span><span class="p">(</span><span class="n" style="color: #333;">top</span><span class="p">,</span> <span class="n" style="color: #333;">ep</span><span class="p">,</span> <span class="n" style="color: #333;">ebwt</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC336" class="line" lang="cpp"> <span class="n" style="color: #333;">ltop</span><span class="p">.</span><span class="n" style="color: #333;">initFromRow</span><span class="p">(</span><span class="n" style="color: #333;">top</span><span class="p">,</span> <span class="n" style="color: #333;">ep</span><span class="p">,</span> <span class="n" style="color: #333;">ebwt</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">prefetch</span></span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC337" class="line" lang="cpp"> <span class="n" style="color: #333;">TIndexOffU</span> <span class="n" style="color: #333;">spread</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bot</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">top</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC338" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Many cache misses on the following lines</span></span>
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<pre style="margin: 0;">-<span id="LC337" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">ltop</span><span class="p">.</span><span class="n" style="color: #333;">_charOff</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">spread</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">sideBwtLen</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC338" class="line" lang="cpp"> <span class="n" style="color: #333;">lbot</span><span class="p">.</span><span class="n" style="color: #333;">_charOff</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="p">)(</span><span class="n" style="color: #333;">ltop</span><span class="p">.</span><span class="n" style="color: #333;">_charOff</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">spread</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC339" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">TIndexOffU</span> <span class="n" style="color: #333;">charOffSum</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ltop</span><span class="p">.</span><span class="n" style="color: #333;">_charOff</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">spread</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC340" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">charOffSum</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">sideBwtLen</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC341" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">bcharOff</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="p">)</span> <span class="n" style="color: #333;">charOffSum</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC342" class="line" lang="cpp"> <span class="n" style="color: #333;">lbot</span><span class="p">.</span><span class="n" style="color: #333;">_charOff</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bcharOff</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC343" class="line" lang="cpp"> <span class="n" style="color: #333;">lbot</span><span class="p">.</span><span class="n" style="color: #333;">_sideNum</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ltop</span><span class="p">.</span><span class="n" style="color: #333;">_sideNum</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC344" class="line" lang="cpp"> <span class="n" style="color: #333;">lbot</span><span class="p">.</span><span class="n" style="color: #333;">_sideByteOff</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ltop</span><span class="p">.</span><span class="n" style="color: #333;">_sideByteOff</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC341" class="line" lang="cpp"> <span class="n" style="color: #333;">lbot</span><span class="p">.</span><span class="n" style="color: #333;">_by</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">lbot</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">_</span>charOff</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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<pre style="margin: 0;">+<span id="LC345" class="line" lang="cpp"> <span class="n" style="color: #333;">lbot</span><span class="p">.</span><span class="n" style="color: #333;">_by</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left right">b</span>charOff</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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<pre style="margin: 0;"> <span id="LC346" class="line" lang="cpp"> <span class="n" style="color: #333;">assert_lt</span><span class="p">(</span><span class="n" style="color: #333;">lbot</span><span class="p">.</span><span class="n" style="color: #333;">_by</span><span class="p">,</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)</span><span class="n" style="color: #333;">ep</span><span class="p">.</span><span class="n" style="color: #333;">_sideBwtSz</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC343" class="line" lang="cpp"> <span class="n" style="color: #333;">lbot</span><span class="p">.</span><span class="n" style="color: #333;">_bp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">lbot</span><span class="p">.</span><span class="n" style="color: #333;">_charOff</span> <span class="o" style="font-weight: 600;">&</span> <span class="mi" style="color: #099;">3</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC347" class="line" lang="cpp"> <span class="n" style="color: #333;">lbot</span><span class="p">.</span><span class="n" style="color: #333;">_bp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bcharOff</span> <span class="o" style="font-weight: 600;">&</span> <span class="mi" style="color: #099;">3</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC348" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// no need for any prefetch, same _sideByteOff</span></span>
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<pre style="margin: 0;"> <span id="LC349" 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="LC345" class="line" lang="cpp"> <span class="n" style="color: #333;">lbot</span><span class="p">.</span><span class="n" style="color: #333;">initFromRow</span><span class="p">(</span><span class="n" style="color: #333;">bot</span><span class="p">,</span> <span class="n" style="color: #333;">ep</span><span class="p">,</span> <span class="n" style="color: #333;">ebwt</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC350" class="line" lang="cpp"> <span class="n" style="color: #333;">lbot</span><span class="p">.</span><span class="n" style="color: #333;">initFromRow</span><span class="p">(</span><span class="n" style="color: #333;">bot</span><span class="p">,</span> <span class="n" style="color: #333;">ep</span><span class="p">,</span> <span class="n" style="color: #333;">ebwt</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">prefetch</span></span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC351" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC352" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC353" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC354" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">prefetchFromTopBot</span><span class="p">(</span></span>
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355
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<pre style="margin: 0;">+<span id="LC355" class="line" lang="cpp"> <span class="n" style="color: #333;">TIndexOffU</span> <span class="n" style="color: #333;">top</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC356" class="line" lang="cpp"> <span class="n" style="color: #333;">TIndexOffU</span> <span class="n" style="color: #333;">bot</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC357" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">EbwtParams</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">ep</span><span class="p">,</span></span>
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358
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<pre style="margin: 0;">+<span id="LC358" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uint8_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">ebwt</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC359" class="line" lang="cpp"> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC360" class="line" lang="cpp"> <span class="n" style="color: #333;">prefetchFromRow</span><span class="p">(</span><span class="n" style="color: #333;">top</span><span class="p">,</span> <span class="n" style="color: #333;">ep</span><span class="p">,</span> <span class="n" style="color: #333;">ebwt</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC361" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// not trying to be smart... prefetches are cheap</span></span>
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<pre style="margin: 0;">+<span id="LC362" class="line" lang="cpp"> <span class="n" style="color: #333;">prefetchFromRow</span><span class="p">(</span><span class="n" style="color: #333;">bot</span><span class="p">,</span> <span class="n" style="color: #333;">ep</span><span class="p">,</span> <span class="n" style="color: #333;">ebwt</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC363" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC364" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC365" 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="LC366" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Calculate SideLocus based on a row and other relevant</span></span>
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<pre style="margin: 0;"> <span id="LC367" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * information about the shape of the Ebwt.</span></span>
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<pre style="margin: 0;"> <span id="LC368" 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="LC353" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">initFromRow</span><span class="p">(</span><span class="n" style="color: #333;">TIndexOffU</span> <span class="n" style="color: #333;">row</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">EbwtParams</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">ep</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uint8_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">ebwt</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC369" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">initFromRow</span><span class="p">(</span><span class="n" style="color: #333;">TIndexOffU</span> <span class="n" style="color: #333;">row</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC370" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">EbwtParams</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">ep</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC371" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uint8_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">ebwt</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC372" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">prefetch</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">true</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC373" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">sideSz</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ep</span><span class="p">.</span><span class="n" style="color: #333;">_sideSz</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC374" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Side length is hard-coded for now; this allows the compiler</span></span>
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<pre style="margin: 0;"> <span id="LC375" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// to do clever things to accelerate / and %.</span></span>
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<pre style="margin: 0;">-<span id="LC357" class="line" lang="cpp"> <span class="n" style="color: #333;">_sideNum</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">row</span> <span class="o" style="font-weight: 600;">/</span> <span class="p">(</span><span class="mi" style="color: #099;">48</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">OFF_SIZE</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC358" class="line" lang="cpp"> <span class="n" style="color: #333;">assert_lt</span><span class="p">(</span><span class="n" style="color: #333;">_sideNum</span><span class="p">,</span> <span class="n" style="color: #333;">ep</span><span class="p">.</span><span class="n" style="color: #333;">_numSides</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC359" class="line" lang="cpp"> <span class="n" style="color: #333;">_charOff</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">row</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="mi" style="color: #099;">48</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">OFF_SIZE</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC360" class="line" lang="cpp"> <span class="n" style="color: #333;">_sideByteOff</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_sideNum</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">sideSz</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC376" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">TIndexOffU</span> <span class="n" style="color: #333;">sideNum</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">row</span> <span class="o" style="font-weight: 600;">/</span> <span class="p">(</span><span class="mi" style="color: #099;">48</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">OFF_SIZE</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;">assert_lt</span><span class="p">(</span><span class="n" style="color: #333;">sideNum</span><span class="p">,</span> <span class="n" style="color: #333;">ep</span><span class="p">.</span><span class="n" style="color: #333;">_numSides</span><span class="p">);</span></span>
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378
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<pre style="margin: 0;">+<span id="LC378" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">charOff</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">row</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="mi" style="color: #099;">48</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">OFF_SIZE</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC379" class="line" lang="cpp"> <span class="n" style="color: #333;">_sideNum</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sideNum</span><span class="p">;</span></span>
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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;">_charOff</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">charOff</span><span class="p">;</span></span>
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381
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<pre style="margin: 0;">+<span id="LC381" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">TIndexOffU</span> <span class="n" style="color: #333;">sByteOff</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sideNum</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">sideSz</span><span class="p">;</span></span>
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382
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<pre style="margin: 0;">+<span id="LC382" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">prefetch</span><span class="p">)</span> <span class="p">{</span></span>
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383
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<pre style="margin: 0;">+<span id="LC383" class="line" lang="cpp"> <span class="n" style="color: #333;">__builtin_prefetch</span><span class="p">(</span><span class="n" style="color: #333;">ebwt</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">sByteOff</span><span class="p">);</span></span>
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384
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<pre style="margin: 0;">+<span id="LC384" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#if (OFF_SIZE>4)</span></span>
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385
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<pre style="margin: 0;">+<span id="LC385" class="line" lang="cpp"> <span class="n" style="color: #333;">__builtin_prefetch</span><span class="p">(</span><span class="n" style="color: #333;">ebwt</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">sByteOff</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">64</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">//64 byte cache lines</span></span>
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386
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<pre style="margin: 0;">+<span id="LC386" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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387
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<pre style="margin: 0;">+<span id="LC387" class="line" lang="cpp"> <span class="p">}</span></span>
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388
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<pre style="margin: 0;">+<span id="LC388" class="line" lang="cpp"></span>
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389
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<pre style="margin: 0;">+<span id="LC389" class="line" lang="cpp"> <span class="n" style="color: #333;">_sideByteOff</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sByteOff</span><span class="p">;</span></span>
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361
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390
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<pre style="margin: 0;"> <span id="LC390" class="line" lang="cpp"> <span class="n" style="color: #333;">assert_leq</span><span class="p">(</span><span class="n" style="color: #333;">row</span><span class="p">,</span> <span class="n" style="color: #333;">ep</span><span class="p">.</span><span class="n" style="color: #333;">_len</span><span class="p">);</span></span>
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362
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391
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<pre style="margin: 0;"> <span id="LC391" class="line" lang="cpp"> <span class="n" style="color: #333;">assert_leq</span><span class="p">(</span><span class="n" style="color: #333;">_sideByteOff</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">sideSz</span><span class="p">,</span> <span class="n" style="color: #333;">ep</span><span class="p">.</span><span class="n" style="color: #333;">_ebwtTotSz</span><span class="p">);</span></span>
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363
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392
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<pre style="margin: 0;"> <span id="LC392" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Tons of cache misses on the next line</span></span>
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364
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<pre style="margin: 0;">-<span id="LC364" class="line" lang="cpp"> <span class="n" style="color: #333;">_by</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left right">_</span>charOff</span> <span class="o" style="font-weight: 600;">>></span> <span class="mi" style="color: #099;">2</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// byte within side</span></span>
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393
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<pre style="margin: 0;">+<span id="LC393" class="line" lang="cpp"> <span class="n" style="color: #333;">_by</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">charOff</span> <span class="o" style="font-weight: 600;">>></span> <span class="mi" style="color: #099;">2</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// byte within side</span></span>
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365
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394
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<pre style="margin: 0;"> <span id="LC394" class="line" lang="cpp"> <span class="n" style="color: #333;">assert_lt</span><span class="p">(</span><span class="n" style="color: #333;">_by</span><span class="p">,</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)</span><span class="n" style="color: #333;">ep</span><span class="p">.</span><span class="n" style="color: #333;">_sideBwtSz</span><span class="p">);</span></span>
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366
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<pre style="margin: 0;">-<span id="LC366" class="line" lang="cpp"> <span class="n" style="color: #333;">_bp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_charOff</span> <span class="o" style="font-weight: 600;">&</span> <span class="mi" style="color: #099;">3</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// bit-pair within byte</span></span>
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395
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<pre style="margin: 0;">+<span id="LC395" class="line" lang="cpp"> <span class="n" style="color: #333;">_bp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">charOff</span> <span class="o" style="font-weight: 600;">&</span> <span class="mi" style="color: #099;">3</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// bit-pair within byte</span></span>
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396
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<pre style="margin: 0;">+<span id="LC396" class="line" lang="cpp"> <span class="p">}</span></span>
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397
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<pre style="margin: 0;">+<span id="LC397" class="line" lang="cpp"></span>
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398
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<pre style="margin: 0;">+<span id="LC398" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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399
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<pre style="margin: 0;">+<span id="LC399" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Prefetch cache lines used by side(row). </span></span>
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<pre style="margin: 0;">+<span id="LC400" 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="LC401" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">prefetchFromRow</span><span class="p">(</span><span class="n" style="color: #333;">TIndexOffU</span> <span class="n" style="color: #333;">row</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">EbwtParams</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">ep</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uint8_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">ebwt</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC402" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">sideSz</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ep</span><span class="p">.</span><span class="n" style="color: #333;">_sideSz</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC403" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Side length is hard-coded for now; this allows the compiler</span></span>
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<pre style="margin: 0;">+<span id="LC404" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// to do clever things to accelerate / and %.</span></span>
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<pre style="margin: 0;">+<span id="LC405" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">TIndexOffU</span> <span class="n" style="color: #333;">sideNum</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">row</span> <span class="o" style="font-weight: 600;">/</span> <span class="p">(</span><span class="mi" style="color: #099;">48</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">OFF_SIZE</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC406" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">TIndexOffU</span> <span class="n" style="color: #333;">sideByteOff</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sideNum</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">sideSz</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC407" class="line" lang="cpp"> <span class="n" style="color: #333;">__builtin_prefetch</span><span class="p">(</span><span class="n" style="color: #333;">ebwt</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">sideByteOff</span><span class="p">);</span></span>
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408
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<pre style="margin: 0;">+<span id="LC408" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#if (OFF_SIZE>4)</span></span>
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409
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<pre style="margin: 0;">+<span id="LC409" class="line" lang="cpp"> <span class="n" style="color: #333;">__builtin_prefetch</span><span class="p">(</span><span class="n" style="color: #333;">ebwt</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">sideByteOff</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">64</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">//64 byte cache lines</span></span>
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410
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<pre style="margin: 0;">+<span id="LC410" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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<pre style="margin: 0;">+<span id="LC411" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC412" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC413" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">prefetch</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uint8_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">ebwt</span><span class="p">)</span> <span class="k" style="font-weight: 600;">const</span> <span class="p">{</span></span>
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414
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<pre style="margin: 0;">+<span id="LC414" class="line" lang="cpp"> <span class="n" style="color: #333;">__builtin_prefetch</span><span class="p">(</span><span class="n" style="color: #333;">ebwt</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">_sideByteOff</span><span class="p">);</span></span>
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415
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<pre style="margin: 0;">+<span id="LC415" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#if (OFF_SIZE>4)</span></span>
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416
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<pre style="margin: 0;">+<span id="LC416" class="line" lang="cpp"> <span class="n" style="color: #333;">__builtin_prefetch</span><span class="p">(</span><span class="n" style="color: #333;">ebwt</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">_sideByteOff</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">64</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">//64 byte cache lines</span></span>
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417
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<pre style="margin: 0;">+<span id="LC417" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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<pre style="margin: 0;"> <span id="LC418" class="line" lang="cpp"> <span class="p">}</span></span>
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419
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<pre style="margin: 0;"> <span id="LC419" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC420" class="line" lang="cpp"> <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">@@ -614,8 +665,8 @@ public:</td>
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<pre style="margin: 0;"> <span id="LC665" class="line" lang="cpp"> <span class="n" style="color: #333;">ProcessorSupport</span> <span class="n" style="color: #333;">ps</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC666" class="line" lang="cpp"> <span class="n" style="color: #333;">_usePOPCNTinstruction</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ps</span><span class="p">.</span><span class="n" style="color: #333;">POPCNTenabled</span><span class="p">();</span></span>
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<pre style="margin: 0;"> <span id="LC667" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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<pre style="margin: 0;">-<span id="LC617" class="line" lang="cpp"> <span class="n" style="color: #333;">_in1Str</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">file</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">".1."</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">gEbwt_ext</span><span class="p">;</span></span>
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618
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<pre style="margin: 0;">-<span id="LC618" class="line" lang="cpp"> <span class="n" style="color: #333;">_in2Str</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">file</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">".2."</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">gEbwt_ext</span><span class="p">;</span></span>
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668
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<pre style="margin: 0;">+<span id="LC668" class="line" lang="cpp"> <span class="n" style="color: #333;">_in1Str</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">file</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">".1."</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">gEbwt_ext</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">".tmp"</span></span><span class="p">;</span></span>
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669
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<pre style="margin: 0;">+<span id="LC669" class="line" lang="cpp"> <span class="n" style="color: #333;">_in2Str</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">file</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">".2."</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">gEbwt_ext</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">".tmp"</span></span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC670" class="line" lang="cpp"> <span class="n" style="color: #333;">packed_</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">packed</span><span class="p">;</span></span>
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671
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<pre style="margin: 0;"> <span id="LC671" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Open output files</span></span>
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672
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<pre style="margin: 0;"> <span id="LC672" class="line" lang="cpp"> <span class="n" style="color: #333;">ofstream</span> <span class="n" style="color: #333;">fout1</span><span class="p">(</span><span class="n" style="color: #333;">_in1Str</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">(),</span> <span class="n" style="color: #333;">ios</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">binary</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1018" style="width: 35px; color: rgba(0,0,0,0.3); 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="1069" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -1018,6 +1069,7 @@ public:</td>
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1018
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1069
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<pre style="margin: 0;"> <span id="LC1069" class="line" lang="cpp"> <span class="n" style="color: #333;">streampos</span> <span class="n" style="color: #333;">out1pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">out1</span><span class="p">.</span><span class="n" style="color: #333;">tellp</span><span class="p">();</span></span>
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1019
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1070
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<pre style="margin: 0;"> <span id="LC1070" class="line" lang="cpp"> <span class="n" style="color: #333;">streampos</span> <span class="n" style="color: #333;">out2pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">out2</span><span class="p">.</span><span class="n" style="color: #333;">tellp</span><span class="p">();</span></span>
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1020
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1071
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<pre style="margin: 0;"> <span id="LC1071" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Look for bmax/dcv parameters that work.</span></span>
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1072
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<pre style="margin: 0;">+<span id="LC1072" class="line" lang="cpp"> <span class="n" style="color: #333;">thread_pool</span> <span class="n" style="color: #333;">pool</span><span class="p">(</span><span class="n" style="color: #333;">nthreads</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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1021
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1073
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<pre style="margin: 0;"> <span id="LC1073" 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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1022
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1074
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<pre style="margin: 0;"> <span id="LC1074" 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;">first</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">bmax</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">40</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">_passMemExc</span><span class="p">)</span> <span class="p">{</span></span>
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1023
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1075
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<pre style="margin: 0;"> <span id="LC1075" 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;">"Could not find approrpiate bmax/dcv settings for building this index."</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1081" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -1081,7 +1133,7 @@ public:</td>
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1081
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1133
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<pre style="margin: 0;"> <span id="LC1133" class="line" lang="cpp"> <span class="n" style="color: #333;">VMSG_NL</span><span class="p">(</span><span class="s" style="color: #d14;">""</span><span class="p">);</span></span>
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1082
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1134
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<pre style="margin: 0;"> <span id="LC1134" class="line" lang="cpp"> <span class="p">}</span></span>
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1083
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1135
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<pre style="margin: 0;"> <span id="LC1135" class="line" lang="cpp"> <span class="n" style="color: #333;">VMSG_NL</span><span class="p">(</span><span class="s" style="color: #d14;">"Constructing suffix-array element generator"</span><span class="p">);</span></span>
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1084
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<pre style="margin: 0;">-<span id="LC1084" class="line" lang="cpp"> <span class="n" style="color: #333;">KarkkainenBlockwiseSA</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">TStr</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">bsa</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">,</span> <span class="n" style="color: #333;">bmax</span><span class="p">,</span> <span class="n" style="color: #333;">nthreads</span><span class="p">,</span> <span class="n" style="color: #333;">dcv</span><span class="p">,</span> <span class="n" style="color: #333;">seed</span><span class="p">,</span> <span class="n" style="color: #333;">_sanity</span><span class="p">,</span> <span class="n" style="color: #333;">_passMemExc</span><span class="p">,</span> <span class="n" style="color: #333;">_verbose</span><span class="p">,</span> <span class="n" style="color: #333;">outfile</span><span class="p">);</span></span>
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1136
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<pre style="margin: 0;">+<span id="LC1136" class="line" lang="cpp"> <span class="n" style="color: #333;">KarkkainenBlockwiseSA</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">TStr</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">bsa</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">,</span> <span class="n" style="color: #333;">bmax</span><span class="p">,</span> <span class="n" style="color: #333;">nthreads</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">pool</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">dcv</span><span class="p">,</span> <span class="n" style="color: #333;">seed</span><span class="p">,</span> <span class="n" style="color: #333;">_sanity</span><span class="p">,</span> <span class="n" style="color: #333;">_passMemExc</span><span class="p">,</span> <span class="n" style="color: #333;">_verbose</span><span class="p">,</span> <span class="n" style="color: #333;">outfile</span><span class="p">);</span></span>
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1085
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1137
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<pre style="margin: 0;"> <span id="LC1137" class="line" lang="cpp"> <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">bsa</span><span class="p">.</span><span class="n" style="color: #333;">suffixItrIsReset</span><span class="p">());</span></span>
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1086
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1138
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<pre style="margin: 0;"> <span id="LC1138" class="line" lang="cpp"> <span class="n" style="color: #333;">assert_eq</span><span class="p">(</span><span class="n" style="color: #333;">bsa</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">(),</span> <span class="n" style="color: #333;">s</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;">1</span><span class="p">);</span></span>
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1087
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1139
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<pre style="margin: 0;"> <span id="LC1139" class="line" lang="cpp"> <span class="n" style="color: #333;">VMSG_NL</span><span class="p">(</span><span class="s" style="color: #d14;">"Converting suffix-array elements to index image"</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1854" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -1802,6 +1854,7 @@ public:</td>
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1802
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1854
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<pre style="margin: 0;"> <span id="LC1854" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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1803
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1855
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<pre style="margin: 0;"> <span id="LC1855" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * This is a performance-critical function. This is the top search-</span></span>
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1804
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1856
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<pre style="margin: 0;"> <span id="LC1856" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * related hit in the time profile.</span></span>
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1857
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<pre style="margin: 0;">+<span id="LC1857" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * The bottleneck seems to be cache misses due to random memory access pattern.</span></span>
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1805
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1858
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<pre style="margin: 0;"> <span id="LC1858" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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1806
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1859
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<pre style="margin: 0;"> <span id="LC1859" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Function gets 11.09% in profile</span></span>
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1807
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1860
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<pre style="margin: 0;"> <span id="LC1860" 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 new_line" data-linenumber="1955" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1902,6 +1955,10 @@ public:</td>
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1902
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1955
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<pre style="margin: 0;"> <span id="LC1955" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Counts the number of occurrences of all four nucleotides in the</span></span>
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1903
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1956
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<pre style="margin: 0;"> <span id="LC1956" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * given side up to (but not including) the given byte/bitpair (by/bp).</span></span>
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1904
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1957
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<pre style="margin: 0;"> <span id="LC1957" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Count for 'a' goes in arrs[0], 'c' in arrs[1], etc.</span></span>
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1958
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<pre style="margin: 0;">+<span id="LC1958" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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1959
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<pre style="margin: 0;">+<span id="LC1959" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * This is a performance-critical function. This is the top search-</span></span>
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1960
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<pre style="margin: 0;">+<span id="LC1960" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * related hit in the time profile.</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1961" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1961
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<pre style="margin: 0;">+<span id="LC1961" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * The bottleneck seems to be cache misses due to random memory access pattern.</span></span>
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1905
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1962
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<pre style="margin: 0;"> <span id="LC1962" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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1906
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1963
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<pre style="margin: 0;"> <span id="LC1963" class="line" lang="cpp"> <span class="kr" style="font-weight: 600;">inline</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">countUpToEx</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">SideLocus</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;">TIndexOffU</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">arrs</span><span class="p">)</span> <span class="k" style="font-weight: 600;">const</span> <span class="p">{</span></span>
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1907
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1964
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<pre style="margin: 0;"> <span id="LC1964" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2010" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2067" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2010,6 +2067,9 @@ public:</td>
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2010
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2067
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<pre style="margin: 0;"> <span id="LC2067" class="line" lang="cpp"> <span class="n" style="color: #333;">assert_eq</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">tops</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]);</span> <span class="n" style="color: #333;">assert_eq</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">bots</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]);</span></span>
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2011
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2068
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<pre style="margin: 0;"> <span id="LC2068" class="line" lang="cpp"> <span class="n" style="color: #333;">assert_eq</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">tops</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]);</span> <span class="n" style="color: #333;">assert_eq</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">bots</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]);</span></span>
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2012
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2069
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<pre style="margin: 0;"> <span id="LC2069" class="line" lang="cpp"> <span class="n" style="color: #333;">assert_eq</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">tops</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]);</span> <span class="n" style="color: #333;">assert_eq</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">bots</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]);</span></span>
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2070
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<pre style="margin: 0;">+<span id="LC2070" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// hopefully ltop and lbot were already prefetched</span></span>
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2071
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<pre style="margin: 0;">+<span id="LC2071" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// if not, we have time to prefetch lbot while procssing ltop</span></span>
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2072
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<pre style="margin: 0;">+<span id="LC2072" class="line" lang="cpp"> <span class="n" style="color: #333;">lbot</span><span class="p">.</span><span class="n" style="color: #333;">prefetch</span><span class="p">(</span><span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">ebwt</span><span class="p">());</span></span>
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2013
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2073
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<pre style="margin: 0;"> <span id="LC2073" class="line" lang="cpp"> <span class="n" style="color: #333;">countBt2SideEx</span><span class="p">(</span><span class="n" style="color: #333;">ltop</span><span class="p">,</span> <span class="n" style="color: #333;">tops</span><span class="p">);</span></span>
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2014
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2074
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<pre style="margin: 0;"> <span id="LC2074" class="line" lang="cpp"> <span class="n" style="color: #333;">countBt2SideEx</span><span class="p">(</span><span class="n" style="color: #333;">lbot</span><span class="p">,</span> <span class="n" style="color: #333;">bots</span><span class="p">);</span></span>
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2015
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2075
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<pre style="margin: 0;"> <span id="LC2075" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#ifndef NDEBUG</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2345" style="width: 35px; color: rgba(0,0,0,0.3); 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="2405" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -2345,7 +2405,7 @@ public:</td>
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2345
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2405
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<pre style="margin: 0;"> <span id="LC2405" class="line" lang="cpp"> <span class="n" style="color: #333;">assert_lt</span><span class="p">(</span><span class="n" style="color: #333;">_zEbwtBpOff</span><span class="p">,</span> <span class="mi" style="color: #099;">4</span><span class="p">);</span></span>
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2346
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2406
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<pre style="margin: 0;"> <span id="LC2406" class="line" lang="cpp"> <span class="n" style="color: #333;">assert_lt</span><span class="p">(</span><span class="n" style="color: #333;">_zEbwtByteOff</span><span class="p">,</span> <span class="n" style="color: #333;">eh</span><span class="p">.</span><span class="n" style="color: #333;">_ebwtTotSz</span><span class="p">);</span></span>
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<td class="old_line diff-line-num" data-linenumber="2347" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2347
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2407
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<pre style="margin: 0;"> <span id="LC2407" class="line" lang="cpp"> <span class="n" style="color: #333;">assert_lt</span><span class="p">(</span><span class="n" style="color: #333;">_zOff</span><span class="p">,</span> <span class="n" style="color: #333;">eh</span><span class="p">.</span><span class="n" style="color: #333;">_bwtLen</span><span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="2348" 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">
2348
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<td class="new_line diff-line-num old" data-linenumber="2408" 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="LC2348" class="line" lang="cpp"> <span class="n" style="color: #333;">assert_geq</span><span class="p">(</span><span class="n" style="color: #333;">_nFrag</span><span class="p">,</span> <span class="n" style="color: #333;">_nPat</span><span class="p">);</span></span>
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2408
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<pre style="margin: 0;">+<span id="LC2408" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">// </span>assert_geq(_nFrag, _nPat);</span></span>
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2349
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2409
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<pre style="margin: 0;"> <span id="LC2409" 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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2350
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2410
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<pre style="margin: 0;"> <span id="LC2410" class="line" lang="cpp"> <span class="p">}</span></span>
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2411
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<pre style="margin: 0;"> <span id="LC2411" class="line" lang="cpp"></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2594" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -2534,9 +2594,6 @@ TStr Ebwt::join(EList<FileBuf*>& l,</td>
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2534
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2594
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<pre style="margin: 0;"> <span id="LC2594" class="line" lang="cpp"> <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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2535
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2595
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<pre style="margin: 0;"> <span id="LC2595" class="line" lang="cpp"> <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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2536
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2596
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<pre style="margin: 0;"> <span id="LC2596" 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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2537
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<td class="new_line diff-line-num old" data-linenumber="2597" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC2537" 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="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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2538
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<pre style="margin: 0;">-<span id="LC2538" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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2539
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<pre style="margin: 0;">-<span id="LC2539" class="line" lang="cpp"> <span class="p">}</span></span>
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2540
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2597
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<pre style="margin: 0;"> <span id="LC2597" class="line" lang="cpp"> <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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2541
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2598
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<pre style="margin: 0;"> <span id="LC2598" class="line" lang="cpp"> <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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2542
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2599
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<pre style="margin: 0;"> <span id="LC2599" class="line" lang="cpp"> <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 old_line" data-linenumber="2581" style="width: 35px; color: rgba(0,0,0,0.3); 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="2638" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2581,10 +2638,10 @@ void Ebwt::joinToDisk(</td>
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2581
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2638
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<pre style="margin: 0;"> <span id="LC2638" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_nFrag</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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2582
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2639
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<pre style="margin: 0;"> <span id="LC2639" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="n" style="color: #333;">TIndexOffU</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;">szs</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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2583
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2640
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<pre style="margin: 0;"> <span id="LC2640" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</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="mi" style="color: #099;">0</span><span class="p">)</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_nFrag</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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2584
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<td class="new_line diff-line-num old" data-linenumber="2641" 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="LC2584" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</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;">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">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">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="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_nPat</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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2641
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<pre style="margin: 0;">+<span id="LC2641" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</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;">first</span><span class="p">)</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_nPat</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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2585
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2642
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<pre style="margin: 0;"> <span id="LC2642" class="line" lang="cpp"> <span class="p">}</span></span>
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2586
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2643
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<pre style="margin: 0;"> <span id="LC2643" class="line" lang="cpp"> <span class="n" style="color: #333;">assert_gt</span><span class="p">(</span><span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_nPat</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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2587
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<pre style="margin: 0;">-<span id="LC2587" class="line" lang="cpp"> <span class="n" style="color: #333;">assert_geq</span><span class="p">(</span><span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_nFrag</span><span class="p">,</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_nPat</span><span class="p">);</span></span>
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2644
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<pre style="margin: 0;">+<span id="LC2644" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">// </span>assert_geq(this->_nFrag, this->_nPat);</span></span>
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2588
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2645
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<pre style="margin: 0;"> <span id="LC2645" class="line" lang="cpp"> <span class="n" style="color: #333;">_rstarts</span><span class="p">.</span><span class="n" style="color: #333;">reset</span><span class="p">();</span></span>
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2589
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2646
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<pre style="margin: 0;"> <span id="LC2646" class="line" lang="cpp"> <span class="n" style="color: #333;">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="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_nPat</span><span class="p">,</span> <span class="n" style="color: #333;">_switchEndian</span><span class="p">);</span></span>
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2590
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2647
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<pre style="margin: 0;"> <span id="LC2647" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Allocate plen[]</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2598" style="width: 35px; color: rgba(0,0,0,0.3); 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="2655" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -2598,15 +2655,12 @@ void Ebwt::joinToDisk(</td>
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2598
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2655
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<pre style="margin: 0;"> <span id="LC2655" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// For each pattern, set plen</span></span>
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2599
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<td class="new_line diff-line-num" data-linenumber="2656" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2656
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<pre style="margin: 0;"> <span id="LC2656" class="line" lang="cpp"> <span class="n" style="color: #333;">TIndexOff</span> <span class="n" style="color: #333;">npat</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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2600
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2657
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<pre style="margin: 0;"> <span id="LC2657" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="n" style="color: #333;">TIndexOffU</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;">szs</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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2601
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<pre style="margin: 0;">-<span id="LC2601" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</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;">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">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">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="p">{</span></span>
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2658
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<pre style="margin: 0;">+<span id="LC2658" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</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;">first</span><span class="p">)</span> <span class="p">{</span></span>
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2602
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2659
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<pre style="margin: 0;"> <span id="LC2659" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">npat</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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2603
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2660
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<pre style="margin: 0;"> <span id="LC2660" class="line" lang="cpp"> <span class="n" style="color: #333;">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="k" style="font-weight: 600;">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;">_switchEndian</span><span class="p">);</span></span>
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2604
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2661
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<pre style="margin: 0;"> <span id="LC2661" class="line" lang="cpp"> <span class="p">}</span></span>
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2605
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2662
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<pre style="margin: 0;"> <span id="LC2662" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">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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2606
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<pre style="margin: 0;">-<span id="LC2606" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">szs</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="p">{</span></span>
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2607
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<pre style="margin: 0;">-<span id="LC2607" class="line" lang="cpp"> <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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2608
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<pre style="margin: 0;">-<span id="LC2608" class="line" lang="cpp"> <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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2609
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<pre style="margin: 0;">-<span id="LC2609" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">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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2663
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<pre style="margin: 0;">+<span id="LC2663" 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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2610
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2664
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<pre style="margin: 0;"> <span id="LC2664" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">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="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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2611
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2665
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<pre style="margin: 0;"> <span id="LC2665" class="line" lang="cpp"> <span class="p">}</span></span>
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2612
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2666
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<pre style="margin: 0;"> <span id="LC2666" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2687" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -2633,7 +2687,7 @@ void Ebwt::joinToDisk(</td>
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2633
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2687
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<pre style="margin: 0;"> <span id="LC2687" class="line" lang="cpp"> <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 class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">_refnames</span><span class="p">.</span><span class="n" style="color: #333;">back</span><span class="p">());</span></span>
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2634
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2688
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<pre style="margin: 0;"> <span id="LC2688" 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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2635
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2689
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<pre style="margin: 0;"> <span id="LC2689" class="line" lang="cpp"> <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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2636
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<pre style="margin: 0;">-<span id="LC2636" 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="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="p">{</span></span>
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2690
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<pre style="margin: 0;">+<span id="LC2690" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">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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2637
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2691
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<pre style="margin: 0;"> <span id="LC2691" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">_refnames</span><span class="p">.</span><span class="n" style="color: #333;">back</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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2638
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2692
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<pre style="margin: 0;"> <span id="LC2692" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// If name was empty, replace with an index</span></span>
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2639
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2693
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<pre style="margin: 0;"> <span id="LC2693" class="line" lang="cpp"> <span class="n" style="color: #333;">ostringstream</span> <span class="n" style="color: #333;">stm</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2643" style="width: 35px; color: rgba(0,0,0,0.3); 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="2697" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -2643,18 +2697,16 @@ void Ebwt::joinToDisk(</td>
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2643
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2697
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<pre style="margin: 0;"> <span id="LC2697" 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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2644
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2698
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<pre style="margin: 0;"> <span id="LC2698" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// This record didn't actually start a new sequence so</span></span>
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2645
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2699
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<pre style="margin: 0;"> <span id="LC2699" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// no need to add a name</span></span>
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2646
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<pre style="margin: 0;">-<span id="LC2646" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//assert_eq(0, _refnames.back().length());</span></span>
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2700
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<pre style="margin: 0;">+<span id="LC2700" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//<span class="idiff left right"> </span>assert_eq(0, _refnames.back().length());</span></span>
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2647
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2701
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<pre style="margin: 0;"> <span id="LC2701" class="line" lang="cpp"> <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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2648
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2702
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<pre style="margin: 0;"> <span id="LC2702" class="line" lang="cpp"> <span class="p">}</span></span>
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2649
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<pre style="margin: 0;">-<span id="LC2649" 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="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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2650
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<pre style="margin: 0;">-<span id="LC2650" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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2651
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<pre style="margin: 0;">-<span id="LC2651" class="line" lang="cpp"> <span class="p">}</span></span>
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2652
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2703
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<pre style="margin: 0;"> <span id="LC2703" class="line" lang="cpp"> <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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2653
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2704
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<pre style="margin: 0;"> <span id="LC2704" class="line" lang="cpp"> <span class="n" style="color: #333;">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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2654
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2705
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<pre style="margin: 0;"> <span id="LC2705" class="line" lang="cpp"> <span class="n" style="color: #333;">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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2655
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2706
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<pre style="margin: 0;"> <span id="LC2706" class="line" lang="cpp"> <span class="n" style="color: #333;">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;">first</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;">first</span><span class="p">);</span></span>
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2656
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2707
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<pre style="margin: 0;"> <span id="LC2707" class="line" lang="cpp"> <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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2657
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2708
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<pre style="margin: 0;"> <span id="LC2708" class="line" lang="cpp"> <span class="n" style="color: #333;">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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2709
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<pre style="margin: 0;">+<span id="LC2709" class="line" lang="cpp"></span>
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2658
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2710
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<pre style="margin: 0;"> <span id="LC2710" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Increment seqsRead if this is the first fragment</span></span>
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2659
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2711
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<pre style="margin: 0;"> <span id="LC2711" 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;">seqsRead</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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2660
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2712
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<pre style="margin: 0;"> <span id="LC2712" class="line" lang="cpp"> <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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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2807" style="width: 35px; color: rgba(0,0,0,0.3); 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="2859" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -2807,7 +2859,6 @@ void Ebwt::buildToDisk(</td>
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2807
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2859
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<pre style="margin: 0;"> <span id="LC2859" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Write length word</span></span>
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2808
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2860
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<pre style="margin: 0;"> <span id="LC2860" class="line" lang="cpp"> <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="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">bwtOut</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;">1</span><span class="p">,</span> <span class="n" style="color: #333;">_switchEndian</span><span class="p">);</span></span>
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2809
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2861
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<pre style="margin: 0;"> <span id="LC2861" class="line" lang="cpp"> <span class="p">}</span></span>
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2810
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<pre style="margin: 0;">-<span id="LC2810" class="line" lang="cpp"></span>
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2811
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2862
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<pre style="margin: 0;"> <span id="LC2862" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span><span class="p">(</span><span class="n" style="color: #333;">side</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">ebwtTotSz</span><span class="p">)</span> <span class="p">{</span></span>
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2812
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<td class="new_line diff-line-num" data-linenumber="2863" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2863
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<pre style="margin: 0;"> <span id="LC2863" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Sanity-check our cursor into the side buffer</span></span>
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2813
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2864
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<pre style="margin: 0;"> <span id="LC2864" class="line" lang="cpp"> <span class="n" style="color: #333;">assert_geq</span><span class="p">(</span><span class="n" style="color: #333;">sideCur</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -21,6 +21,7 @@</td>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="cpp"></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 <string></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 <iostream></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 <fstream></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 <getopt.h></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 <stdexcept></span></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="cpp"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -38,8 +39,9 @@ static int names_only = 0; // just print the sequence names in the index</td>
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<pre style="margin: 0;"> <span id="LC39" 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;">summarize_only</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;">// just print summary of index and quit</span></span>
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<pre style="margin: 0;"> <span id="LC40" 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;">across</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">60</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// number of characters across in FASTA output</span></span>
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<pre style="margin: 0;"> <span id="LC41" 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;">refFromEbwt</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;">// true -> when printing reference, decode it from Ebwt instead of reading it from BitPairReference</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">out_filename</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// name of output file</span></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">wrapper</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC42" 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;">"vhnsea:"</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC44" 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;">"vhnsea:<span class="idiff left right">o:</span>"</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="cpp"><span class="k" style="font-weight: 600;">enum</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="cpp"> <span class="n" style="color: #333;">ARG_VERSION</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">256</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">@@ -56,6 +58,7 @@ static struct option long_options[] = {</td>
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<pre style="margin: 0;"> <span id="LC58" 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;">"help"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="sc" style="color: #d14;">'h'</span><span class="p">},</span></span>
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<pre style="margin: 0;"> <span id="LC59" 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;">"across"</span><span class="p">,</span> <span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="sc" style="color: #d14;">'a'</span><span class="p">},</span></span>
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60
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<pre style="margin: 0;"> <span id="LC60" 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;">"ebwt-ref"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="sc" style="color: #d14;">'e'</span><span class="p">},</span></span>
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61
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<pre style="margin: 0;">+<span id="LC61" 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;">"output"</span><span class="p">,</span> <span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="sc" style="color: #d14;">'o'</span><span class="p">},</span></span>
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59
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62
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<pre style="margin: 0;"> <span id="LC62" 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;">"wrapper"</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_WRAPPER</span><span class="p">},</span></span>
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60
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63
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<pre style="margin: 0;"> <span id="LC63" 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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61
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64
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="cpp"><span class="p">};</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="76" style="width: 35px; color: rgba(0,0,0,0.3); 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="79" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -76,23 +79,23 @@ static void printUsage(ostream& out) {</td>
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76
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79
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<pre style="margin: 0;"> <span id="LC79" 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>
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77
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80
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">wrapper</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"basic-0"</span><span class="p">)</span> <span class="p">{</span></span>
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78
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81
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="cpp"> <span class="n" style="color: #333;">out</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" --large-index force inspection of the 'large' index, even if a"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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79
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<pre style="margin: 0;">-<span id="LC79" class="line" lang="cpp"> <span class="idiff left right"> </span><span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" 'small' one is present."</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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80
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<pre style="margin: 0;">-<span id="LC80" class="line" lang="cpp"> <span class="idiff left right"> </span><span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" --debug use the debug binary; slower, assertions enabled"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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81
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<pre style="margin: 0;">-<span id="LC81" class="line" lang="cpp"> <span class="idiff left right"> </span><span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" --sanitized use sanitized binary; slower, uses ASan and/or UBSan"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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82
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<pre style="margin: 0;">-<span id="LC82" class="line" lang="cpp"> <span class="idiff left right"> </span><span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" --verbose log the issued command"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="82" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="cpp"> <span class="idiff left right"> </span><span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" 'small' one is present."</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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<td class="new_line diff-line-num new" data-linenumber="83" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="cpp"> <span class="idiff left right"> </span><span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" --debug use the debug binary; slower, assertions enabled"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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<td class="new_line diff-line-num new" data-linenumber="84" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="cpp"> <span class="idiff left right"> </span><span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" --sanitized use sanitized binary; slower, uses ASan and/or UBSan"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="cpp"> <span class="idiff left right"> </span><span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" --verbose log the issued command"</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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83
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86
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="cpp"> <span class="p">}</span></span>
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84
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87
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<pre style="margin: 0;"> <span id="LC87" class="line" lang="cpp"> <span class="n" style="color: #333;">out</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" -a/--across <int> Number of characters across in FASTA output (default: 60)"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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85
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<pre style="margin: 0;">-<span id="LC85" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" -n/--names Print reference sequence names only"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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86
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<pre style="margin: 0;">-<span id="LC86" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" -s/--summary Print summary incl. ref names, lengths, index properties"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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<pre style="margin: 0;">-<span id="LC87" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" -<span class="idiff left">v</span>/--<span class="idiff">verbose</span> <span class="idiff">Verbos</span>e output <span class="idiff right">(for debugging</span>)"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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88
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<pre style="margin: 0;">-<span id="LC88" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" -<span class="idiff left">h</span>/--<span class="idiff right">help print detailed description of tool and its options</span>"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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89
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<pre style="margin: 0;">-<span id="LC89" class="line" lang="cpp"> <span class="p">;</span></span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="cpp"> <span class="idiff left right"> </span><span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" -n/--names Print reference sequence names only"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="cpp"> <span class="idiff left right"> </span><span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" -s/--summary Print summary incl. ref names, lengths, index properties"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="cpp"> <span class="idiff left"> </span><span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" -<span class="idiff">o</span>/--<span class="idiff">output</span> <span class="idiff"> Sav</span>e output <span class="idiff right">to filename (default stdout</span>)"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="cpp"> <span class="idiff left"> </span><span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" -<span class="idiff">v</span>/--<span class="idiff right">verbose Verbose output (for debugging)</span>"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="cpp"> <span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff"><<</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">" -h/--help print this and message quit"</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 right">endl</span></span><span class="p">;</span></span>
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90
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93
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<pre style="margin: 0;"> <span id="LC93" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">wrapper</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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94
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<pre style="margin: 0;"> <span id="LC94" class="line" lang="cpp"> <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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92
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95
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<pre style="margin: 0;"> <span id="LC95" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"*** Warning ***"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span></span>
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<pre style="margin: 0;">-<span id="LC93" class="line" lang="cpp"> <span class="idiff left right"> </span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"'boowtie2-inspect' was run directly. It is recommended "</span></span>
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94
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<pre style="margin: 0;">-<span id="LC94" class="line" lang="cpp"> <span class="idiff left right"> </span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"to use the wrapper script instead."</span></span>
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95
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<pre style="margin: 0;">-<span id="LC95" class="line" lang="cpp"> <span class="idiff left right"> </span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="cpp"> <span class="idiff left right"> </span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"'boowtie2-inspect' was run directly. It is recommended "</span></span>
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<td class="new_line diff-line-num new" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="cpp"> <span class="idiff left right"> </span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"to use the wrapper script instead."</span></span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="cpp"> <span class="idiff left right"> </span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="cpp"> <span class="p">}</span></span>
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100
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="cpp"><span class="p">}</span></span>
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101
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<pre style="margin: 0;"> <span id="LC101" class="line" lang="cpp"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="141" style="width: 35px; color: rgba(0,0,0,0.3); 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="144" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -141,6 +144,7 @@ static void parseOptions(int argc, char **argv) {</td>
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141
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144
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<pre style="margin: 0;"> <span id="LC144" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'e'</span><span class="p">:</span> <span class="n" style="color: #333;">refFromEbwt</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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142
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145
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<pre style="margin: 0;"> <span id="LC145" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'n'</span><span class="p">:</span> <span class="n" style="color: #333;">names_only</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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143
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146
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<pre style="margin: 0;"> <span id="LC146" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'s'</span><span class="p">:</span> <span class="n" style="color: #333;">summarize_only</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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147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'o'</span><span class="p">:</span> <span class="n" style="color: #333;">out_filename</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">optarg</span><span class="p">;</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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148
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<pre style="margin: 0;"> <span id="LC148" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'a'</span><span class="p">:</span> <span class="n" style="color: #333;">across</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parseInt</span><span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="s" style="color: #d14;">"-a/--across arg must be at least 1"</span><span class="p">);</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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149
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<pre style="margin: 0;"> <span id="LC149" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">:</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/* Done with options. */</span></span>
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150
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<pre style="margin: 0;"> <span id="LC150" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -369,18 +373,21 @@ static void driver(</td>
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373
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<pre style="margin: 0;"> <span id="LC373" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">ebwtFileBase</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="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">query</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC375" class="line" lang="cpp"><span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC372" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Adjust</span></span>
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376
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<pre style="margin: 0;">+<span id="LC376" class="line" lang="cpp"> <span class="n" style="color: #333;">ostream</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fout</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">out_filename</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="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;">:</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">ofstream</span><span class="p">(</span><span class="n" style="color: #333;">out_filename</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="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;">fout</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">good</span><span class="p">())</span> <span class="p">{</span></span>
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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;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Unable to open "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">out_filename</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" for writing."</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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379
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<pre style="margin: 0;">+<span id="LC379" class="line" lang="cpp"> <span class="n" style="color: #333;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC380" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC381" class="line" lang="cpp"> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">adjustedEbwtFileBase</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">adjustEbwtBase</span><span class="p">(</span><span class="n" style="color: #333;">argv0</span><span class="p">,</span> <span class="n" style="color: #333;">ebwtFileBase</span><span class="p">,</span> <span class="n" style="color: #333;">verbose</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC374" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC382" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">names_only</span><span class="p">)</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;">print_index_sequence_names</span><span class="p">(</span><span class="n" style="color: #333;">adjustedEbwtFileBase</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">c</span>out</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC383" class="line" lang="cpp"> <span class="n" style="color: #333;">print_index_sequence_names</span><span class="p">(</span><span class="n" style="color: #333;">adjustedEbwtFileBase</span><span class="p">,</span> <span class="o" style="font-weight: 600;"><span class="idiff left">*</span></span><span class="n" style="color: #333;"><span class="idiff right">f</span>out</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC384" 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;">summarize_only</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC378" class="line" lang="cpp"> <span class="n" style="color: #333;">print_index_summary</span><span class="p">(</span><span class="n" style="color: #333;">adjustedEbwtFileBase</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">c</span>out</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC385" class="line" lang="cpp"> <span class="n" style="color: #333;">print_index_summary</span><span class="p">(</span><span class="n" style="color: #333;">adjustedEbwtFileBase</span><span class="p">,</span> <span class="o" style="font-weight: 600;"><span class="idiff left">*</span></span><span class="n" style="color: #333;"><span class="idiff right">f</span>out</span><span class="p">);</span></span>
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386
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<pre style="margin: 0;"> <span id="LC386" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC387" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Initialize Ebwt object</span></span>
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388
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<pre style="margin: 0;"> <span id="LC388" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">color</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">readEbwtColor</span><span class="p">(</span><span class="n" style="color: #333;">adjustedEbwtFileBase</span><span class="p">);</span></span>
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382
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389
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<pre style="margin: 0;"> <span id="LC389" class="line" lang="cpp"> <span class="n" style="color: #333;">Ebwt</span> <span class="n" style="color: #333;">ebwt</span><span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC383" class="line" lang="cpp"> <span class="n" style="color: #333;">adjustedEbwtFileBase</span><span class="p">,</span><span class="idiff left right"> </span></span>
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390
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<pre style="margin: 0;">+<span id="LC390" class="line" lang="cpp"> <span class="n" style="color: #333;">adjustedEbwtFileBase</span><span class="p">,</span></span>
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384
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<pre style="margin: 0;"> <span id="LC391" class="line" lang="cpp"> <span class="n" style="color: #333;">color</span><span class="p">,</span> <span class="c1" style="color: #998; font-style: italic;">// index is colorspace</span></span>
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392
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<pre style="margin: 0;"> <span id="LC392" class="line" lang="cpp"> <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;">// don't care about entire-reverse</span></span>
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<pre style="margin: 0;"> <span id="LC393" class="line" lang="cpp"> <span class="nb" style="color: #0086b3;">true</span><span class="p">,</span> <span class="c1" style="color: #998; font-style: italic;">// index is for the forward direction</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="412" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -412,7 +419,7 @@ static void driver(</td>
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419
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<pre style="margin: 0;"> <span id="LC419" class="line" lang="cpp"> <span class="n" style="color: #333;">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;">refnames</span><span class="p">;</span></span>
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420
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<pre style="margin: 0;"> <span id="LC420" class="line" lang="cpp"> <span class="n" style="color: #333;">readEbwtRefnames</span><span class="p">(</span><span class="n" style="color: #333;">adjustedEbwtFileBase</span><span class="p">,</span> <span class="n" style="color: #333;">refnames</span><span class="p">);</span></span>
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414
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421
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<pre style="margin: 0;"> <span id="LC421" class="line" lang="cpp"> <span class="n" style="color: #333;">print_ref_sequences</span><span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC415" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left right">c</span>out</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC422" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><span class="idiff left">*</span></span><span class="n" style="color: #333;"><span class="idiff right">f</span>out</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC423" class="line" lang="cpp"> <span class="n" style="color: #333;">readEbwtColor</span><span class="p">(</span><span class="n" style="color: #333;">ebwtFileBase</span><span class="p">),</span></span>
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424
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<pre style="margin: 0;"> <span id="LC424" class="line" lang="cpp"> <span class="n" style="color: #333;">refnames</span><span class="p">,</span></span>
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425
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<pre style="margin: 0;"> <span id="LC425" class="line" lang="cpp"> <span class="n" style="color: #333;">ebwt</span><span class="p">.</span><span class="n" style="color: #333;">plen</span><span class="p">(),</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="429" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -422,6 +429,10 @@ static void driver(</td>
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429
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<pre style="margin: 0;"> <span id="LC429" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">ebwt</span><span class="p">.</span><span class="n" style="color: #333;">isInMemory</span><span class="p">())</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC430" class="line" lang="cpp"> <span class="n" style="color: #333;">ebwt</span><span class="p">.</span><span class="n" style="color: #333;">evictFromMemory</span><span class="p">();</span></span>
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<pre style="margin: 0;"> <span id="LC431" class="line" lang="cpp"> <span class="p">}</span></span>
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432
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<pre style="margin: 0;">+<span id="LC432" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">fout</span> <span class="o" style="font-weight: 600;">!=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">cout</span><span class="p">)</span> <span class="p">{</span></span>
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433
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<pre style="margin: 0;">+<span id="LC433" class="line" lang="cpp"> <span class="p">((</span><span class="n" style="color: #333;">ofstream</span> <span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">fout</span><span class="p">)</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">close</span><span class="p">();</span></span>
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434
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<pre style="margin: 0;">+<span id="LC434" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">delete</span> <span class="n" style="color: #333;">fout</span><span class="p">;</span></span>
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435
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<pre style="margin: 0;">+<span id="LC435" class="line" lang="cpp"> <span class="p">}</span></span>
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436
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<pre style="margin: 0;"> <span id="LC436" class="line" lang="cpp"> <span class="p">}</span></span>
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437
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<pre style="margin: 0;"> <span id="LC437" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC438" class="line" lang="cpp"></span>
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<a href="https://salsa.debian.org/med-team/bowtie2/-/commit/cf277464ee949fe563ca814a827b2387be02dbd1#64f1aac6be9dd64453121ce3592c43407e567ded"><strong>bt2_io.cpp</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="287" style="width: 35px; color: rgba(0,0,0,0.3); 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="287" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -287,7 +287,7 @@ void Ebwt::readIntoMemory(</td>
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287
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287
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<pre style="margin: 0;"> <span id="LC287" 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;">"Reading rstarts ("</span> <span class="o" style="font-weight: 600;"><<</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_nFrag</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="s" style="color: #d14;">"): "</span><span class="p">;</span></span>
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288
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288
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<pre style="margin: 0;"> <span id="LC288" class="line" lang="cpp"> <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>
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289
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289
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<pre style="margin: 0;"> <span id="LC289" class="line" lang="cpp"> <span class="p">}</span></span>
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290
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<pre style="margin: 0;">-<span id="LC290" class="line" lang="cpp"> <span class="n" style="color: #333;">assert_geq</span><span class="p">(</span><span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_nFrag</span><span class="p">,</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">_nPat</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC290" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">// </span>assert_geq(this->_nFrag, this->_nPat);</span></span>
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291
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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;">_rstarts</span><span class="p">.</span><span class="n" style="color: #333;">reset</span><span class="p">();</span></span>
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292
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292
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<pre style="margin: 0;"> <span id="LC292" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">loadRstarts</span><span class="p">)</span> <span class="p">{</span></span>
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293
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293
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<pre style="margin: 0;"> <span id="LC293" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">_useMm</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="695" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -695,9 +695,9 @@ readEbwtRefnames(FILE* fin, EList<string>& refnames) {</td>
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695
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695
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<pre style="margin: 0;"> <span id="LC695" 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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696
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696
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<pre style="margin: 0;"> <span id="LC696" 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="o" style="font-weight: 600;">=</span> <span class="sc" style="color: #d14;">'\0'</span><span class="p">;</span></span>
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697
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697
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<pre style="margin: 0;"> <span id="LC697" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">read_value</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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698
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<pre style="margin: 0;">-<span id="LC698" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">read_value</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fgetc</span><span class="p">(</span><span class="n" style="color: #333;">fin</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC698" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">read_value</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fgetc</span><span class="p">(</span><span class="n" style="color: #333;">fin</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC699" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">read_value</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">EOF</span><span class="p">)</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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700
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<pre style="margin: 0;">-<span id="LC700" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">read_value</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC700" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">read_value</span><span class="p">;</span></span>
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701
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701
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<pre style="margin: 0;"> <span id="LC701" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'\0'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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702
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702
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<pre style="margin: 0;"> <span id="LC702" class="line" lang="cpp"> <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;">c</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'\n'</span><span class="p">)</span> <span class="p">{</span></span>
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703
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<pre style="margin: 0;"> <span id="LC703" class="line" lang="cpp"> <span class="n" style="color: #333;">refnames</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="s" style="color: #d14;">""</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="713" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -713,7 +713,7 @@ readEbwtRefnames(FILE* fin, EList<string>& refnames) {</td>
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<pre style="margin: 0;"> <span id="LC713" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC714" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC715" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Be kind</span></span>
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<pre style="margin: 0;">-<span id="LC716" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">fseeko</span><span class="p">(</span><span class="n" style="color: #333;">fin</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">SEEK_SET</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC716" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">fseeko</span><span class="p">(</span><span class="n" style="color: #333;">fin</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">SEEK_SET</span><span class="p">);</span></span>
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717
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<pre style="margin: 0;"> <span id="LC717" class="line" lang="cpp"> <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">ferror</span><span class="p">(</span><span class="n" style="color: #333;">fin</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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718
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<pre style="margin: 0;"> <span id="LC718" class="line" lang="cpp"><span class="p">}</span></span>
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719
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719
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<pre style="margin: 0;"> <span id="LC719" class="line" lang="cpp"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="935" style="width: 35px; color: rgba(0,0,0,0.3); 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="935" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -935,10 +935,11 @@ void Ebwt::szsToDisk(const EList<RefRecord>& szs, ostream& os, int reverse) {</td>
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935
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<pre style="margin: 0;"> <span id="LC935" class="line" lang="cpp"> <span class="n" style="color: #333;">TIndexOffU</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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936
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<pre style="margin: 0;"> <span id="LC936" class="line" lang="cpp"> <span class="n" style="color: #333;">TIndexOffU</span> <span class="n" style="color: #333;">totlen</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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937
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937
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<pre style="margin: 0;"> <span id="LC937" 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;">unsigned</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;">szs</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC938" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</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="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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939
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938
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<pre style="margin: 0;"> <span id="LC938" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</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;">first</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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940
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939
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<pre style="margin: 0;"> <span id="LC939" 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;">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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941
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<pre style="margin: 0;">-<span id="LC941" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</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;">first</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;">len</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;">seq</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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940
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<pre style="margin: 0;">+<span id="LC940" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</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;">first</span><span class="p">)</span> <span class="n" style="color: #333;">seq</span><span class="o" style="font-weight: 600;">++</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;">if</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="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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942
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<pre style="margin: 0;">+<span id="LC942" class="line" lang="cpp"></span>
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942
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943
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<pre style="margin: 0;"> <span id="LC943" class="line" lang="cpp"> <span class="n" style="color: #333;">TIndexOffU</span> <span class="n" style="color: #333;">seqm1</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="mi" style="color: #099;">1</span><span class="p">;</span></span>
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943
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<pre style="margin: 0;"> <span id="LC944" class="line" lang="cpp"> <span class="n" style="color: #333;">assert_lt</span><span class="p">(</span><span class="n" style="color: #333;">seqm1</span><span class="p">,</span> <span class="n" style="color: #333;">_nPat</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC945" class="line" lang="cpp"> <span class="n" style="color: #333;">TIndexOffU</span> <span class="n" style="color: #333;">fwoff</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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<a href="https://salsa.debian.org/med-team/bowtie2/-/commit/cf277464ee949fe563ca814a827b2387be02dbd1#9f15b0fe50d277c8d231ce47c6a42a8355f51ff0"><strong>diff_sample.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">@@ -30,6 +30,7 @@</td>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "mem_ids.h"</span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "ls.h"</span></span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "btypes.h"</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "threadpool.h"</span></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="cpp"><span class="k" style="font-weight: 600;">using</span> <span class="k" style="font-weight: 600;">namespace</span> <span class="n" style="color: #333;">std</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="cpp"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -506,7 +507,7 @@ public:</td>
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507
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<pre style="margin: 0;"> <span id="LC507" class="line" lang="cpp"> <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="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">dmap</span><span class="p">()</span> <span class="k" style="font-weight: 600;">const</span> <span class="p">{</span> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">_dmap</span><span class="p">;</span> <span class="p">}</span></span>
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508
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<pre style="margin: 0;"> <span id="LC508" class="line" lang="cpp"> <span class="n" style="color: #333;">ostream</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">log</span><span class="p">()</span> <span class="k" style="font-weight: 600;">const</span> <span class="p">{</span> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">_logger</span><span class="p">;</span> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC509" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC509" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">build</span><span class="p">(</span><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="LC510" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">build</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">thread_pool</span></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">pool</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><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="LC511" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">tieBreakOff</span><span class="p">(</span><span class="n" style="color: #333;">TIndexOffU</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">TIndexOffU</span> <span class="n" style="color: #333;">j</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="LC512" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int64_t</span> <span class="n" style="color: #333;">breakTie</span><span class="p">(</span><span class="n" style="color: #333;">TIndexOffU</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">TIndexOffU</span> <span class="n" style="color: #333;">j</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="LC513" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">isCovered</span><span class="p">(</span><span class="n" style="color: #333;">TIndexOffU</span> <span class="n" style="color: #333;">i</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="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -740,7 +741,7 @@ public:</td>
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<pre style="margin: 0;"> <span id="LC741" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * packed according to the mu mapping, in _isaPrime.</span></span>
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<pre style="margin: 0;"> <span id="LC742" 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="LC743" class="line" lang="cpp"><span class="k" style="font-weight: 600;">template</span> <span class="o" style="font-weight: 600;"><</span><span class="k" style="font-weight: 600;">typename</span> <span class="nc" style="color: #458; font-weight: 600;">TStr</span><span class="p">></span></span>
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<pre style="margin: 0;">-<span id="LC743" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">DifferenceCoverSample</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">TStr</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">build</span><span class="p">(</span><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="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC744" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">DifferenceCoverSample</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">TStr</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">build</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">thread_pool</span></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">pool</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><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="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC745" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Local names for relevant types</span></span>
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<pre style="margin: 0;"> <span id="LC746" class="line" lang="cpp"> <span class="n" style="color: #333;">VMSG_NL</span><span class="p">(</span><span class="s" style="color: #d14;">"Building DifferenceCoverSample"</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC747" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Local names for relevant data</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">@@ -806,7 +807,7 @@ void DifferenceCoverSample<TStr>::build(int nthreads) {</td>
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807
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<pre style="margin: 0;"> <span id="LC807" class="line" lang="cpp"> <span class="n" style="color: #333;">mkeyQSortSuf2</span><span class="p">(</span><span class="n" style="color: #333;">t</span><span class="p">,</span> <span class="n" style="color: #333;">sPrimeArr</span><span class="p">,</span> <span class="n" style="color: #333;">sPrimeSz</span><span class="p">,</span> <span class="n" style="color: #333;">sPrimeOrderArr</span><span class="p">,</span> <span class="mi" style="color: #099;">4</span><span class="p">,</span></span>
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808
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<pre style="margin: 0;"> <span id="LC808" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">verbose</span><span class="p">(),</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">,</span> <span class="n" style="color: #333;">query_depth</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">boundaries</span><span class="p">);</span></span>
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809
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<pre style="margin: 0;"> <span id="LC809" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">boundaries</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC809" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">AutoArray</span></span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="n" style="color: #333;"><span class="idiff">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="kr" style="font-weight: 600;"><span class="idiff">thread</span></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">threads</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff right">nthreads</span></span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC810" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">vector</span></span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="n" style="color: #333;"><span class="idiff">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">future</span></span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">void</span></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="n" style="color: #333;"><span class="idiff">threads</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">pool</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">size</span></span><span class="p"><span class="idiff right">()</span>);</span></span>
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811
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<pre style="margin: 0;"> <span id="LC811" class="line" lang="cpp"> <span class="n" style="color: #333;">EList</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">VSortingParam</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">TStr</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">tparams</span><span class="p">;</span></span>
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811
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812
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<pre style="margin: 0;"> <span id="LC812" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">cur</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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812
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813
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<pre style="margin: 0;"> <span id="LC813" class="line" lang="cpp"> <span class="n" style="color: #333;">MUTEX_T</span> <span class="n" style="color: #333;">mutex</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">@@ -822,13 +823,14 @@ void DifferenceCoverSample<TStr>::build(int nthreads) {</td>
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822
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823
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<pre style="margin: 0;"> <span id="LC823" class="line" lang="cpp"> <span class="n" style="color: #333;">tparams</span><span class="p">[</span><span class="n" style="color: #333;">tid</span><span class="p">].</span><span class="n" style="color: #333;">boundaries</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">boundaries</span><span class="p">;</span></span>
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823
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824
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<pre style="margin: 0;"> <span id="LC824" class="line" lang="cpp"> <span class="n" style="color: #333;">tparams</span><span class="p">[</span><span class="n" style="color: #333;">tid</span><span class="p">].</span><span class="n" style="color: #333;">cur</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">cur</span><span class="p">;</span></span>
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825
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<pre style="margin: 0;"> <span id="LC825" class="line" lang="cpp"> <span class="n" style="color: #333;">tparams</span><span class="p">[</span><span class="n" style="color: #333;">tid</span><span class="p">].</span><span class="n" style="color: #333;">mutex</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">mutex</span><span class="p">;</span></span>
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825
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<pre style="margin: 0;">-<span id="LC825" class="line" lang="cpp"> <span class="n" style="color: #333;">threads</span><span class="p">[</span><span class="n" style="color: #333;">tid</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kr" style="font-weight: 600;">thread</span><span class="p">(</span><span class="n" style="color: #333;">VSorting_worker</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">TStr</span><span class="o" style="font-weight: 600;">></span><span class="p">(((</span><span class="kt" style="color: #458; font-weight: 600;">void</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;">tparams</span><span class="p">[</span><span class="n" style="color: #333;">tid</span><span class="p">])));</span></span>
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826
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<pre style="margin: 0;">+<span id="LC826" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">tid</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">nthreads</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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827
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<pre style="margin: 0;">+<span id="LC827" class="line" lang="cpp"> <span class="n" style="color: #333;">VSorting_worker</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">TStr</span><span class="o" style="font-weight: 600;">></span><span class="p">(((</span><span class="kt" style="color: #458; font-weight: 600;">void</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;">tparams</span><span class="p">[</span><span class="n" style="color: #333;">tid</span><span class="p">]));</span></span>
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828
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<pre style="margin: 0;">+<span id="LC828" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span></span>
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829
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<pre style="margin: 0;">+<span id="LC829" class="line" lang="cpp"> <span class="n" style="color: #333;">threads</span><span class="p">[</span><span class="n" style="color: #333;">tid</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pool</span><span class="p">.</span><span class="n" style="color: #333;">submit</span><span class="p">(</span><span class="n" style="color: #333;">VSorting_worker</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">TStr</span><span class="o" style="font-weight: 600;">></span><span class="p">(((</span><span class="kt" style="color: #458; font-weight: 600;">void</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;">tparams</span><span class="p">[</span><span class="n" style="color: #333;">tid</span><span class="p">])));</span></span>
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826
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830
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<pre style="margin: 0;"> <span id="LC830" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC827" 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;">tid</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;">tid</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;"><span class="idiff left right">nthreads</span></span><span class="p">;</span> <span class="n" style="color: #333;">tid</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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828
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<pre style="margin: 0;">-<span id="LC828" class="line" lang="cpp"> <span class="n" style="color: #333;">threads</span><span class="p">[</span><span class="n" style="color: #333;">tid</span><span class="p">]</span><span class="o" style="font-weight: 600;"><span class="idiff left">-></span></span><span class="n" style="color: #333;"><span class="idiff right">join</span></span><span class="p">();</span></span>
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831
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<pre style="margin: 0;">+<span id="LC831" 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;">tid</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;">tid</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;"><span class="idiff left">pool</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">size</span></span><span class="p"><span class="idiff right">()</span>;</span> <span class="n" style="color: #333;">tid</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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832
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<pre style="margin: 0;">+<span id="LC832" class="line" lang="cpp"> <span class="n" style="color: #333;">threads</span><span class="p">[</span><span class="n" style="color: #333;">tid</span><span class="p">]<span class="idiff left">.</span></span><span class="n" style="color: #333;"><span class="idiff right">get</span></span><span class="p">();</span></span>
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<pre style="margin: 0;"> <span id="LC833" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC830" 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;">tid</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;">tid</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">nthreads</span><span class="p">;</span> <span class="n" style="color: #333;">tid</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC831" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">delete</span> <span class="n" style="color: #333;">threads</span><span class="p">[</span><span class="n" style="color: #333;">tid</span><span class="p">];</span></span>
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<pre style="margin: 0;"> <span id="LC834" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC835" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">sanityCheck</span><span class="p">())</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC836" class="line" lang="cpp"> <span class="n" style="color: #333;">sanityCheckOrderedSufs</span><span class="p">(</span><span class="n" style="color: #333;">t</span><span class="p">,</span> <span class="n" style="color: #333;">t</span><span class="p">.</span><span class="n" style="color: #333;">length</span><span class="p">(),</span> <span class="n" style="color: #333;">sPrimeArr</span><span class="p">,</span> <span class="n" style="color: #333;">sPrimeSz</span><span class="p">,</span> <span class="n" style="color: #333;">v</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">@@ -1555,6 +1555,14 @@ Sequence-N <name> <len></code></pre></td>
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<pre style="margin: 0;">+<span id="LC1558" class="line" lang="html"><span class="nt" style="color: #000080;"><td</span> <span class="na" style="color: #008080;">id=</span><span class="s" style="color: #d14;">"bowtie2-inspect-options-o"</span><span class="nt" style="color: #000080;">></span></span>
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<pre style="margin: 0;">+<span id="LC1559" class="line" lang="html"><span class="nt" style="color: #000080;"><pre><code></span>-o/--output <span class="ni" style="color: #800080;"><</span>filename<span class="ni" style="color: #800080;">></span><span class="nt" style="color: #000080;"></code></pre></span></span>
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<pre style="margin: 0;">+<span id="LC1562" class="line" lang="html"><span class="nt" style="color: #000080;"><p></span>Save output to user-specified filename (default: stdout)<span class="nt" style="color: #000080;"></p></span></span>
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<pre style="margin: 0;"> <span id="LC1567" class="line" lang="html"><span class="nt" style="color: #000080;"><pre><code></span>-v/--verbose<span class="nt" style="color: #000080;"></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">@@ -1529,6 +1529,14 @@ Sequence-N <name> <len></code></pre></td>
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<pre style="margin: 0;">+<span id="LC1532" class="line" lang="plaintext"><td id="bowtie2-inspect-options-o"></span>
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<pre style="margin: 0;">+<span id="LC1533" class="line" lang="plaintext"><pre><code>-o/--output <filename></code></pre></span>
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<pre style="margin: 0;">+<span id="LC1534" class="line" lang="plaintext"></td></span>
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<pre style="margin: 0;">+<span id="LC1536" class="line" lang="plaintext"><p>Save output to user-specified filename (default: stdout)</p></span>
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<pre style="margin: 0;"> <span id="LC1540" class="line" lang="plaintext"><td></span>
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<pre style="margin: 0;"> <span id="LC1541" class="line" lang="plaintext"><pre><code>-v/--verbose</code></pre></span>
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<br>
</li>
<li id="9485aa1b2c39982f48264019fde0712132ed80f5">
<a href="https://salsa.debian.org/med-team/bowtie2/-/commit/cf277464ee949fe563ca814a827b2387be02dbd1#9485aa1b2c39982f48264019fde0712132ed80f5"><strong>doc/website/recent_news.ssi</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext"><h2>Version 2.4.5 - Jan 16, 2022</h2></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"><h3 id="bowtie2">bowtie2</h3></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"><ul></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> <li>Fixed issues with <code>bowtie2</code> BAM parser that would cause <code>bowtie2</code> to crash when processing input that was encoded with tools other than samtools e.g. Picard.</li></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> <li>Fixed an issue causing <code>bowtie2</code> to drop certain optional fields when when aligning BAM reads with the <code><a href="manual.shtml#bowtie2-options-preserve-tags">--preserve-tags</a></code> option.</li></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> <li>Fixed an issue causing <code>bowtie2</code> to produce mangled SAM output when specifying <code><a href="manual.shtml#bowtie2-options-sam-append-comment">--sam-append-comment</a></code> together with the <code>--passthrough</code> option.</li></span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> <li>Appended <code>GO:query</code> to SAM <code>@HD</code> entry to indicate that reads are grouped by query name, bump SAM version to 1.5 to indicate support for this change.</li></span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"></ul></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"><h3 id="bowtie2-build">bowtie2-build</h3></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>Implemented thread pool to address performance regressions introduced during the switch to C++11 threads.</li></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> <li>Fixed an issue causing masked-sequence metadata to be omitted from index. This issue would subsequently result in sequence data, <code>@SQ</code>, being left out from alignment SAM header.</li></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> <li>Included <code>.tmp</code> extension to index files currenlty being built. The extension is removed only upon successful build. This change seeks to address the assumption that <code>bowtie2-build</code> ran successfully without building the reverse indexes.</li></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"> <li>Fixed an issue causing <code>bowtie2-build</code> to sometimes incorrectly calculate input size. This issue would result in the wrong index type being chosen and only happened with GZip compressed files.</li></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"></ul></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"><h3 id="bowtie2-inspect">bowtie2-inspect</h3></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>Added a new <code><a href="manual.shtml#bowtie2-inspect-options-o">-o/--output</a></code> option to save the output of <code>bowtie2-inspect</code> to a file instead of being dumped to standard output.</li></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"></ul></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext"><h2>Version 2.4.4 - May 23, 2021</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 that would sometimes cause deadlocks in <code>bowtie2</code> when running multithreaded</li></span>
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<li id="59bf596910fb7006481a4d8a45de81ff2bd75a4d">
<a href="https://salsa.debian.org/med-team/bowtie2/-/commit/cf277464ee949fe563ca814a827b2387be02dbd1#59bf596910fb7006481a4d8a45de81ff2bd75a4d"><strong>doc/website/rhsidebar.ssi</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">@@ -18,10 +18,10 @@</td>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="plaintext"> <a href="https://sourceforge.net/projects/bowtie-bio/files/bowtie2/2.4.<span class="idiff left">4</span>">Bowtie2 v2.4.<span class="idiff right">4</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/bowtie2/2.4.<span class="idiff left">5</span>">Bowtie2 v2.4.<span class="idiff right">5</span></a></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="plaintext"> <span class="idiff left">23</span>/0<span class="idiff">5</span>/2<span class="idiff right">1</span> </span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"> <span class="idiff left">16</span>/0<span class="idiff">1</span>/2<span class="idiff right">2</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">@@ -480,16 +480,20 @@ void CFilePatternSource::open() {</td>
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<pre style="margin: 0;"> <span id="LC480" class="line" lang="cpp"> <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;">while</span><span class="p">(</span><span class="n" style="color: #333;">filecur_</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;">size</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="k" style="font-weight: 600;">if</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="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"-"</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC483" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// always assume that data from stdin is compressed</span></span>
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<pre style="margin: 0;">-<span id="LC484" class="line" lang="cpp"> <span class="n" style="color: #333;">compressionType_</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">CompressionType</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">GZIP</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC483" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">fd</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dup</span><span class="p">(</span><span class="n" style="color: #333;">fileno</span><span class="p">(</span><span class="n" style="color: #333;">stdin</span><span class="p">));</span></span>
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<pre style="margin: 0;">-<span id="LC486" 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;">fd</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="LC484" 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;">format</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">BAM</span><span class="p">)</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;">compressionType_</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">CompressionType</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">NONE</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC486" 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;">fdopen</span><span class="p">(</span><span class="n" style="color: #333;">fd</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="LC487" 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="LC488" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// always assume that data from stdin is compressed</span></span>
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<pre style="margin: 0;">+<span id="LC489" class="line" lang="cpp"> <span class="n" style="color: #333;">compressionType_</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">CompressionType</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">GZIP</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC490" 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;">fd</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="LC491" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC488" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</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="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC489" class="line" lang="cpp"> <span class="n" style="color: #333;">close</span><span class="p">(</span><span class="n" style="color: #333;">fd</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC492" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</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="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC493" class="line" lang="cpp"> <span class="n" style="color: #333;">close</span><span class="p">(</span><span class="n" style="color: #333;">fd</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC494" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC495" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC491" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC492" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC496" 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="LC497" 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="LC498" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC499" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">fd</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">open</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="p">,</span> <span class="n" style="color: #333;">O_RDONLY</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">@@ -1274,195 +1278,136 @@ std::pair<bool, int> BAMPatternSource::nextBatch(PerThreadReadBuf& pt, bool batc</td>
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<pre style="margin: 0;"> <span id="LC1278" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint16_t</span> <span class="n" style="color: #333;">cdata_len</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC1279" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">nread</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="LC1280" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC1281" class="line" lang="cpp"> <span class="n" style="color: #333;">ThreadSafe</span> <span class="n" style="color: #333;">ts</span><span class="p">(</span><span class="n" style="color: #333;">mutex</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC1282" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">do</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC1278" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">bam_batch_indexes_</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">pt</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">tid_</span></span><span class="p"><span class="idiff">]</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">>=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">bam_batches_</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">pt</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">tid_</span></span><span class="p"><span class="idiff right">]</span>.</span><span class="n" style="color: #333;">size</span><span class="p">())</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC1283" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">alignment_offset</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 right">alignment_batch</span></span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">())</span> <span class="p">{</span></span>
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1284
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<pre style="margin: 0;"> <span id="LC1284" class="line" lang="cpp"> <span class="n" style="color: #333;">BGZF</span> <span class="n" style="color: #333;">block</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC1280" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">uint8_t</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">batch</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bam_batches_</span><span class="p">[</span><span class="n" style="color: #333;">pt</span><span class="p">.</span><span class="n" style="color: #333;">tid_</span><span class="p">];</span></span>
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<pre style="margin: 0;">-<span id="LC1281" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">lock</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC1282" class="line" lang="cpp"> <span class="n" style="color: #333;">ThreadSafe</span> <span class="n" style="color: #333;">ts</span><span class="p">(</span><span class="n" style="color: #333;">mutex</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC1283" 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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<pre style="margin: 0;">-<span id="LC1284" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// parse the BAM header;</span></span>
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1285
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<pre style="margin: 0;">-<span id="LC1285" class="line" lang="cpp"> <span class="n" style="color: #333;">nextBGZFBlockFromFile</span><span class="p">(</span><span class="n" style="color: #333;">block</span><span class="p">);</span></span>
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1286
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<pre style="margin: 0;">-<span id="LC1286" 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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1287
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<pre style="margin: 0;">-<span id="LC1287" class="line" lang="cpp"> <span class="p">}</span></span>
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1288
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<pre style="margin: 0;">-<span id="LC1288" class="line" lang="cpp"> <span class="n" style="color: #333;">cdata_len</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nextBGZFBlockFromFile</span><span class="p">(</span><span class="n" style="color: #333;">block</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="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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1290
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<pre style="margin: 0;">-<span id="LC1290" 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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1291
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<pre style="margin: 0;">-<span id="LC1291" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// parse the BAM header</span></span>
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<pre style="margin: 0;">-<span id="LC1292" class="line" lang="cpp"> <span class="n" style="color: #333;">nextBGZFBlockFromFile</span><span class="p">(</span><span class="n" style="color: #333;">block</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="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="LC1294" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC1295" class="line" lang="cpp"> <span class="n" style="color: #333;">cdata_len</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nextBGZFBlockFromFile</span><span class="p">(</span><span class="n" style="color: #333;">block</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC1296" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC1285" class="line" lang="cpp"> <span class="n" style="color: #333;">cdata_len</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nextBGZFBlockFromFile</span><span class="p">(</span><span class="n" style="color: #333;">block</span><span class="p">);</span></span>
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1286
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<pre style="margin: 0;"> <span id="LC1286" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">cdata_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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1298
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<pre style="margin: 0;"> <span id="LC1287" class="line" lang="cpp"> <span class="n" style="color: #333;">done</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nread</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="LC1288" 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="LC1289" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC1301" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">bam_batch_indexes_</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">pt</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">tid_</span></span><span class="p"><span class="idiff right">]</span></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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1302
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<pre style="margin: 0;">-<span id="LC1302" class="line" lang="cpp"> <span class="n" style="color: #333;">batch</span><span class="p">.</span><span class="n" style="color: #333;">resize</span><span class="p">(</span><span class="n" style="color: #333;">block</span><span class="p">.</span><span class="n" style="color: #333;">ftr</span><span class="p">.</span><span class="n" style="color: #333;">isize</span><span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1303" 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">
1303
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<pre style="margin: 0;">-<span id="LC1303" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ret_code</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">decompress_bgzf_block</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;"><span class="idiff left">batch</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff right">]</span>,</span> <span class="n" style="color: #333;">block</span><span class="p">.</span><span class="n" style="color: #333;">ftr</span><span class="p">.</span><span class="n" style="color: #333;">isize</span><span class="p">,</span> <span class="n" style="color: #333;">block</span><span class="p">.</span><span class="n" style="color: #333;">cdata</span><span class="p">,</span> <span class="n" style="color: #333;">cdata_len</span><span class="p">);</span></span>
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1290
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<pre style="margin: 0;">+<span id="LC1290" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left right">alignment_offset</span></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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1291
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<pre style="margin: 0;">+<span id="LC1291" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">alignment_</span>batch</span><span class="p">.</span><span class="n" style="color: #333;">resize</span><span class="p">(</span><span class="n" style="color: #333;">block</span><span class="p">.</span><span class="n" style="color: #333;">ftr</span><span class="p">.</span><span class="n" style="color: #333;">isize</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 right">delta_</span></span><span class="p">);</span></span>
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1292
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<pre style="margin: 0;">+<span id="LC1292" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ret_code</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">decompress_bgzf_block</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;"><span class="idiff left">alignment_batch</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">]</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">delta_</span></span><span class="p">,</span> <span class="n" style="color: #333;">block</span><span class="p">.</span><span class="n" style="color: #333;">ftr</span><span class="p">.</span><span class="n" style="color: #333;">isize</span><span class="p">,</span> <span class="n" style="color: #333;">block</span><span class="p">.</span><span class="n" style="color: #333;">cdata</span><span class="p">,</span> <span class="n" style="color: #333;">cdata_len</span><span class="p">);</span></span>
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1304
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1293
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<pre style="margin: 0;"> <span id="LC1293" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">ret_code</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">Z_OK</span><span class="p">)</span> <span class="p">{</span></span>
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1305
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1294
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<pre style="margin: 0;"> <span id="LC1294" 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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1306
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1295
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<pre style="margin: 0;"> <span id="LC1295" class="line" lang="cpp"> <span class="p">}</span></span>
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1296
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<pre style="margin: 0;">+<span id="LC1296" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#ifndef NDEBUG</span></span>
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1307
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1297
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<pre style="margin: 0;"> <span id="LC1297" class="line" lang="cpp"> <span class="n" style="color: #333;">uLong</span> <span class="n" style="color: #333;">crc</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">crc32</span><span class="p">(</span><span class="mi" style="color: #099;">0L</span><span class="p">,</span> <span class="n" style="color: #333;">Z_NULL</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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1308
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<td class="new_line diff-line-num old" data-linenumber="1298" 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="LC1308" class="line" lang="cpp"> <span class="n" style="color: #333;">crc</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">crc32</span><span class="p">(</span><span class="n" style="color: #333;">crc</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;"><span class="idiff left">batch</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">],</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">batch</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">());</span></span>
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1298
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<pre style="margin: 0;">+<span id="LC1298" class="line" lang="cpp"> <span class="n" style="color: #333;">crc</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">crc32</span><span class="p">(</span><span class="n" style="color: #333;">crc</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;"><span class="idiff left">alignment_batch</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">]</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">delta_</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">alignment_</span>batch</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</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 right">delta_</span></span><span class="p">);</span></span>
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1309
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1299
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<pre style="margin: 0;"> <span id="LC1299" class="line" lang="cpp"> <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">crc</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">block</span><span class="p">.</span><span class="n" style="color: #333;">ftr</span><span class="p">.</span><span class="n" style="color: #333;">crc32</span><span class="p">);</span></span>
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1300
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<pre style="margin: 0;">+<span id="LC1300" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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1301
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<pre style="margin: 0;">+<span id="LC1301" class="line" lang="cpp"> <span class="n" style="color: #333;">delta_</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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1310
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1302
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<pre style="margin: 0;"> <span id="LC1302" class="line" lang="cpp"> <span class="p">}</span></span>
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1311
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1303
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<pre style="margin: 0;"> <span id="LC1303" 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;">ret</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">get_alignments</span><span class="p">(</span><span class="n" style="color: #333;">pt</span><span class="p">,</span> <span class="n" style="color: #333;">batch_a</span><span class="p">,</span> <span class="n" style="color: #333;">nread</span><span class="p">,</span> <span class="n" style="color: #333;">lock</span><span class="p">);</span></span>
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1312
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<td class="new_line diff-line-num" data-linenumber="1304" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1304
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<pre style="margin: 0;"> <span id="LC1304" class="line" lang="cpp"> <span class="n" style="color: #333;">done</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ret</span><span class="p">.</span><span class="n" style="color: #333;">first</span><span class="p">;</span></span>
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1313
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1305
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<pre style="margin: 0;"> <span id="LC1305" class="line" lang="cpp"> <span class="p">}</span> <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;">done</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">nread</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>
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1314
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1306
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<pre style="margin: 0;"> <span id="LC1306" class="line" lang="cpp"></span>
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1315
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<pre style="margin: 0;">-<span id="LC1315" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">lock</span><span class="p">)</span> <span class="p">{</span></span>
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1316
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<pre style="margin: 0;">-<span id="LC1316" class="line" lang="cpp"> <span class="n" style="color: #333;">ThreadSafe</span> <span class="n" style="color: #333;">ts</span><span class="p">(</span><span class="n" style="color: #333;">mutex</span><span class="p">);</span></span>
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1317
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<pre style="margin: 0;">-<span id="LC1317" class="line" lang="cpp"> <span class="n" style="color: #333;">pt</span><span class="p">.</span><span class="n" style="color: #333;">setReadId</span><span class="p">(</span><span class="n" style="color: #333;">readCnt_</span><span class="p">);</span></span>
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1318
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<pre style="margin: 0;">-<span id="LC1318" class="line" lang="cpp"> <span class="n" style="color: #333;">readCnt_</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">nread</span><span class="p">;</span></span>
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1319
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<pre style="margin: 0;">-<span id="LC1319" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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1320
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<pre style="margin: 0;">-<span id="LC1320" class="line" lang="cpp"> <span class="n" style="color: #333;">pt</span><span class="p">.</span><span class="n" style="color: #333;">setReadId</span><span class="p">(</span><span class="n" style="color: #333;">readCnt_</span><span class="p">);</span></span>
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1321
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<pre style="margin: 0;">-<span id="LC1321" class="line" lang="cpp"> <span class="n" style="color: #333;">readCnt_</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">nread</span><span class="p">;</span></span>
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1322
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<pre style="margin: 0;">-<span id="LC1322" class="line" lang="cpp"> <span class="p">}</span></span>
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1307
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<pre style="margin: 0;">+<span id="LC1307" class="line" lang="cpp"> <span class="n" style="color: #333;">pt</span><span class="p">.</span><span class="n" style="color: #333;">setReadId</span><span class="p">(</span><span class="n" style="color: #333;">readCnt_</span><span class="p">);</span></span>
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1308
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<pre style="margin: 0;">+<span id="LC1308" class="line" lang="cpp"> <span class="n" style="color: #333;">readCnt_</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">nread</span><span class="p">;</span></span>
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1309
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<pre style="margin: 0;">+<span id="LC1309" class="line" lang="cpp"></span>
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1310
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<pre style="margin: 0;"> <span id="LC1310" 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;">nread</span><span class="p">);</span></span>
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1311
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<pre style="margin: 0;"> <span id="LC1311" class="line" lang="cpp"><span class="p">}</span></span>
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1312
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<pre style="margin: 0;"> <span id="LC1312" class="line" lang="cpp"></span>
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1326
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1313
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<pre style="margin: 0;"> <span id="LC1313" class="line" lang="cpp"><span class="n" style="color: #333;">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;">get_alignments</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="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="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">readi</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">lock</span><span class="p">)</span> <span class="p">{</span></span>
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1327
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<pre style="margin: 0;">-<span id="LC1327" class="line" lang="cpp"> <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;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">bam_batch_indexes_</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">pt</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">tid_</span></span><span class="p"><span class="idiff right">]</span>;</span></span>
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1314
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<pre style="margin: 0;">+<span id="LC1314" class="line" lang="cpp"> <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;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left right">alignment_offset</span></span><span class="p">;</span></span>
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1328
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1315
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<pre style="margin: 0;"> <span id="LC1315" 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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1329
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<pre style="margin: 0;">-<span id="LC1329" 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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1330
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1316
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<pre style="margin: 0;"> <span id="LC1316" class="line" lang="cpp"></span>
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1317
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<pre style="margin: 0;">+<span id="LC1317" 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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1318
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<pre style="margin: 0;">+<span id="LC1318" 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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1319
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<pre style="margin: 0;">+<span id="LC1319" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">l_text</span><span class="p">;</span></span>
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1320
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<pre style="margin: 0;">+<span id="LC1320" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">nref</span><span class="p">;</span></span>
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1321
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<pre style="margin: 0;">+<span id="LC1321" class="line" lang="cpp"></span>
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1322
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<pre style="margin: 0;">+<span id="LC1322" class="line" lang="cpp"> <span class="n" style="color: #333;">memcpy</span><span class="p">(</span><span class="n" style="color: #333;">magic</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">alignment_batch</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="mi" style="color: #099;">4</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1323" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1323
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<pre style="margin: 0;">+<span id="LC1323" class="line" lang="cpp"> <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">magic</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'B'</span><span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">magic</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;">'A'</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">magic</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'M'</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">magic</span><span class="p">[</span><span class="mi" style="color: #099;">3</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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1324
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<pre style="margin: 0;">+<span id="LC1324" 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;">4</span><span class="p">;</span></span>
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1325
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<pre style="margin: 0;">+<span id="LC1325" class="line" lang="cpp"> <span class="n" style="color: #333;">memcpy</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="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">alignment_batch</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">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;">l_text</span><span class="p">));</span></span>
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1326
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<pre style="margin: 0;">+<span id="LC1326" class="line" lang="cpp"> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">+</span> <span class="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;">l_text</span><span class="p">;</span></span>
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1327
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<pre style="margin: 0;">+<span id="LC1327" class="line" lang="cpp"> <span class="n" style="color: #333;">memcpy</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">nref</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">alignment_batch</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">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;">nref</span><span class="p">));</span></span>
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1328
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<pre style="margin: 0;">+<span id="LC1328" class="line" lang="cpp"> <span class="n" style="color: #333;">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;">nref</span><span class="p">);</span></span>
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1329
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<pre style="margin: 0;">+<span id="LC1329" 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;">uint32_t</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">nref</span><span class="p">;</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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1330
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<pre style="margin: 0;">+<span id="LC1330" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">l_name</span><span class="p">;</span></span>
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1331
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<pre style="margin: 0;">+<span id="LC1331" class="line" lang="cpp"> <span class="n" style="color: #333;">memcpy</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="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">alignment_batch</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">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;">l_name</span><span class="p">));</span></span>
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1332
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<pre style="margin: 0;">+<span id="LC1332" class="line" lang="cpp"> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">+</span> <span class="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="n" style="color: #333;">l_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>
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1333
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<pre style="margin: 0;">+<span id="LC1333" class="line" lang="cpp"> <span class="p">}</span></span>
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1334
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<pre style="margin: 0;">+<span id="LC1334" class="line" lang="cpp"> <span class="n" style="color: #333;">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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1335
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<pre style="margin: 0;">+<span id="LC1335" class="line" lang="cpp"> <span class="p">}</span></span>
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1331
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1336
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<pre style="margin: 0;"> <span id="LC1336" 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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<pre style="margin: 0;">-<span id="LC1332" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;"><span class="idiff left">bam_batches_</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">pt</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">tid_</span></span><span class="p"><span class="idiff right">]</span>.</span><span class="n" style="color: #333;">size</span><span class="p">())</span> <span class="p">{</span></span>
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1337
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<pre style="margin: 0;">+<span id="LC1337" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;"><span class="idiff left right">alignment_batch</span></span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">())</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC1338" 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;">false</span><span class="p">,</span> <span class="n" style="color: #333;">readi</span><span class="p">);</span></span>
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1334
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1339
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<pre style="margin: 0;"> <span id="LC1339" class="line" lang="cpp"> <span class="p">}</span></span>
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1340
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<pre style="margin: 0;"> <span id="LC1340" class="line" lang="cpp"></span>
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1336
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1341
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<pre style="margin: 0;"> <span id="LC1341" 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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1337
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<pre style="margin: 0;">-<span id="LC1337" 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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1338
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<pre style="margin: 0;">-<span id="LC1338" 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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1342
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<pre style="margin: 0;">+<span id="LC1342" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">block_size</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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1339
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1343
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<pre style="margin: 0;"> <span id="LC1343" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC1340" 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;">block_size</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">bam_batches_</span><span class="p">[</span><span class="n" style="color: #333;">pt</span><span class="p">.</span><span class="n" style="color: #333;">tid_</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">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;">block_size</span><span class="p">));</span></span>
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1344
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<pre style="margin: 0;">+<span id="LC1344" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">alignment_batch</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="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>
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1345
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<pre style="margin: 0;">+<span id="LC1345" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">next_batch</span><span class="p">;</span></span>
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1346
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<pre style="margin: 0;">+<span id="LC1346" 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;">block_size</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">alignment_batch</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">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;">block_size</span><span class="p">));</span></span>
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1341
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1347
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<pre style="margin: 0;"> <span id="LC1347" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">currentlyBigEndian</span><span class="p">())</span></span>
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1342
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1348
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<pre style="margin: 0;"> <span id="LC1348" class="line" lang="cpp"> <span class="n" style="color: #333;">block_size</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">endianSwapU32</span><span class="p">(</span><span class="n" style="color: #333;">block_size</span><span class="p">);</span></span>
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1343
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<pre style="margin: 0;">-<span id="LC1343" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">block_size</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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1349
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<pre style="margin: 0;">+<span id="LC1349" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">block_size</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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1350
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<pre style="margin: 0;">+<span id="LC1350" 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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1351
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<pre style="margin: 0;">+<span id="LC1351" class="line" lang="cpp"> <span class="p">}</span></span>
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1352
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<pre style="margin: 0;">+<span id="LC1352" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">block_size</span> <span class="o" style="font-weight: 600;">></span> <span class="p">(</span><span class="n" style="color: #333;">alignment_batch</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">i</span> <span class="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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1353
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<pre style="margin: 0;">+<span id="LC1353" class="line" lang="cpp"> <span class="nl">next_batch:</span></span>
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1354
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<pre style="margin: 0;">+<span id="LC1354" class="line" lang="cpp"> <span class="n" style="color: #333;">delta_</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alignment_batch</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">i</span><span class="p">;</span></span>
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1355
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<pre style="margin: 0;">+<span id="LC1355" class="line" lang="cpp"> <span class="n" style="color: #333;">memcpy</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">alignment_batch</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">alignment_batch</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">delta_</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1356" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1356
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<pre style="margin: 0;">+<span id="LC1356" class="line" lang="cpp"> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alignment_batch</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span></span>
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1344
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1357
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<pre style="margin: 0;"> <span id="LC1357" 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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1345
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1358
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<pre style="margin: 0;"> <span id="LC1358" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="old_line diff-line-num" data-linenumber="1346" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1346
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1359
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<pre style="margin: 0;"> <span id="LC1359" class="line" lang="cpp"> <span class="n" style="color: #333;">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;">block_size</span><span class="p">);</span></span>
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1347
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<pre style="margin: 0;">-<span id="LC1347" class="line" lang="cpp"></span>
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1348
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<pre style="margin: 0;">-<span id="LC1348" class="line" lang="cpp"> <span class="n" style="color: #333;">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="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">bam_batches_</span><span class="p">[</span><span class="n" style="color: #333;">pt</span><span class="p">.</span><span class="n" style="color: #333;">tid_</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">i</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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1360
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<pre style="margin: 0;">+<span id="LC1360" 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="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">alignment_batch</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">i</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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1349
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<td class="new_line diff-line-num" data-linenumber="1361" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1361
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<pre style="margin: 0;"> <span id="LC1361" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">currentlyBigEndian</span><span class="p">())</span></span>
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1350
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1362
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<pre style="margin: 0;"> <span id="LC1362" class="line" lang="cpp"> <span class="n" style="color: #333;">flag</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">endianSwapU16</span><span class="p">(</span><span class="n" style="color: #333;">flag</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1363" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1363
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<pre style="margin: 0;">+<span id="LC1363" 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="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;">0x80</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="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="new_line diff-line-num new" data-linenumber="1364" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1364
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<pre style="margin: 0;">+<span id="LC1364" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</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;">0x4</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1365" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1365
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<pre style="margin: 0;">+<span id="LC1365" 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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1366
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<pre style="margin: 0;">+<span id="LC1366" class="line" lang="cpp"> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">block_size</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1367" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1367
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<pre style="margin: 0;">+<span id="LC1367" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1368" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1368
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<pre style="margin: 0;">+<span id="LC1368" class="line" lang="cpp"> <span class="p">}</span></span>
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1351
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<td class="new_line diff-line-num" data-linenumber="1369" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1369
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<pre style="margin: 0;"> <span id="LC1369" 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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<td class="old_line diff-line-num" data-linenumber="1352" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1352
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<td class="new_line diff-line-num" data-linenumber="1370" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1370
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<pre style="margin: 0;"> <span id="LC1370" 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="old_line diff-line-num" data-linenumber="1353" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1353
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<td class="new_line diff-line-num" data-linenumber="1371" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1371
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<pre style="margin: 0;"> <span id="LC1371" class="line" lang="cpp"> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">block_size</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="1354" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1354
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<td class="new_line diff-line-num" data-linenumber="1372" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1372
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<pre style="margin: 0;"> <span id="LC1372" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="1355" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1355
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<td class="new_line diff-line-num" data-linenumber="1373" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1373
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<pre style="margin: 0;"> <span id="LC1373" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1356" 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">
1356
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<td class="new_line diff-line-num old" data-linenumber="1374" 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="LC1356" class="line" lang="cpp"></span>
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<td class="old_line diff-line-num" data-linenumber="1357" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1357
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<td class="new_line diff-line-num" data-linenumber="1374" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1374
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<pre style="margin: 0;"> <span id="LC1374" 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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<td class="old_line diff-line-num" data-linenumber="1358" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1358
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<td class="new_line diff-line-num" data-linenumber="1375" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1375
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<pre style="margin: 0;"> <span id="LC1375" 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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1359
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<td class="new_line diff-line-num" data-linenumber="1376" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1376
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<pre style="margin: 0;"> <span id="LC1376" class="line" lang="cpp"> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">block_size</span><span class="p">;</span></span>
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1360
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<td class="new_line diff-line-num" data-linenumber="1377" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1377
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<pre style="margin: 0;"> <span id="LC1377" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="1361" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1361
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<td class="new_line diff-line-num" data-linenumber="1378" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1378
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<pre style="margin: 0;"> <span id="LC1378" class="line" lang="cpp"> <span class="p">}</span></span>
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1362
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<td class="new_line diff-line-num" data-linenumber="1379" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1379
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<pre style="margin: 0;"> <span id="LC1379" class="line" lang="cpp"></span>
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<td class="old_line diff-line-num old" data-linenumber="1363" 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">
1363
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<td class="new_line diff-line-num old" data-linenumber="1380" 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="LC1363" 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>
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<td class="old_line diff-line-num old" data-linenumber="1364" 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">
1364
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<td class="new_line diff-line-num old" data-linenumber="1380" 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="LC1364" class="line" lang="cpp"> <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="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">block_size</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">bam_batches_</span><span class="p">[</span><span class="n" style="color: #333;">pt</span><span class="p">.</span><span class="n" style="color: #333;">tid_</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>
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<td class="old_line diff-line-num old" data-linenumber="1365" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1365
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<td class="new_line diff-line-num old" data-linenumber="1380" 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="LC1365" class="line" lang="cpp"> <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="o" style="font-weight: 600;">&&</span> <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;">block_size</span><span class="p">))))</span></span>
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1366
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<td class="new_line diff-line-num old" data-linenumber="1380" 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="LC1366" class="line" lang="cpp"> <span class="p">{</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1367" 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">
1367
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<td class="new_line diff-line-num old" data-linenumber="1380" 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="LC1367" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">lock</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1368" 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">
1368
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<td class="new_line diff-line-num old" data-linenumber="1380" 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="LC1368" class="line" lang="cpp"> <span class="n" style="color: #333;">ThreadSafe</span> <span class="n" style="color: #333;">ts</span><span class="p">(</span><span class="n" style="color: #333;">orphan_mates_mutex_</span><span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1369" 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">
1369
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<td class="new_line diff-line-num old" data-linenumber="1380" 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="LC1369" class="line" lang="cpp"> <span class="n" style="color: #333;">get_or_store_orhaned_mate</span><span class="p">(</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 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="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">bam_batches_</span><span class="p">[</span><span class="n" style="color: #333;">pt</span><span class="p">.</span><span class="n" style="color: #333;">tid_</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">block_size</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC1370" class="line" lang="cpp"> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">block_size</span><span class="p">;</span></span>
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1371
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<pre style="margin: 0;">-<span id="LC1371" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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1372
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<pre style="margin: 0;">-<span id="LC1372" class="line" lang="cpp"> <span class="n" style="color: #333;">get_or_store_orhaned_mate</span><span class="p">(</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 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="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">bam_batches_</span><span class="p">[</span><span class="n" style="color: #333;">pt</span><span class="p">.</span><span class="n" style="color: #333;">tid_</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">block_size</span><span class="p">);</span></span>
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1373
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<pre style="margin: 0;">-<span id="LC1373" class="line" lang="cpp"> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">block_size</span><span class="p">;</span></span>
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1374
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<pre style="margin: 0;">-<span id="LC1374" class="line" lang="cpp"> <span class="p">}</span></span>
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1375
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<pre style="margin: 0;">-<span id="LC1375" class="line" lang="cpp"></span>
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1376
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<td class="new_line diff-line-num old" data-linenumber="1380" 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="LC1376" 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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1377
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<pre style="margin: 0;">-<span id="LC1377" 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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1378
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<pre style="margin: 0;">-<span id="LC1378" class="line" lang="cpp"></span>
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1379
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<pre style="margin: 0;">-<span id="LC1379" class="line" lang="cpp"> <span class="n" style="color: #333;">memcpy</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="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">bam_batches_</span><span class="p">[</span><span class="n" style="color: #333;">pt</span><span class="p">.</span><span class="n" style="color: #333;">tid_</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">block_size</span><span class="p">);</span></span>
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1380
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<pre style="margin: 0;">-<span id="LC1380" class="line" lang="cpp"> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">block_size</span><span class="p">;</span></span>
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1381
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<pre style="margin: 0;">-<span id="LC1381" class="line" lang="cpp"></span>
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1382
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<td class="new_line diff-line-num old" data-linenumber="1380" 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="LC1382" 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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1383
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<td class="new_line diff-line-num old" data-linenumber="1380" 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="LC1383" 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 class="o" style="font-weight: 600;">&&</span></span>
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1384
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<pre style="margin: 0;">-<span id="LC1384" class="line" lang="cpp"> <span class="n" style="color: #333;">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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1385
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<pre style="margin: 0;">-<span id="LC1385" class="line" lang="cpp"> <span class="p">}</span></span>
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1380
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<pre style="margin: 0;">+<span id="LC1380" 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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1381
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<pre style="margin: 0;">+<span id="LC1381" class="line" lang="cpp"> <span class="n" style="color: #333;">memcpy</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="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">alignment_batch</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">block_size</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC1382" class="line" lang="cpp"> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">block_size</span><span class="p">;</span></span>
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1383
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<pre style="margin: 0;">+<span id="LC1383" class="line" lang="cpp"> <span class="n" style="color: #333;">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 class="o" style="font-weight: 600;">&&</span></span>
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1384
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<pre style="margin: 0;">+<span id="LC1384" class="line" lang="cpp"> <span class="n" style="color: #333;">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="mi" style="color: #099;">0</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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1386
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1385
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<pre style="margin: 0;"> <span id="LC1385" class="line" lang="cpp"> <span class="p">}</span></span>
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1387
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1386
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<pre style="margin: 0;"> <span id="LC1386" class="line" lang="cpp"></span>
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1388
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1387
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<pre style="margin: 0;"> <span id="LC1387" 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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1389
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1388
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<pre style="margin: 0;"> <span id="LC1388" class="line" lang="cpp"><span class="p">}</span></span>
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1390
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1389
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<pre style="margin: 0;"> <span id="LC1389" class="line" lang="cpp"></span>
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1391
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<pre style="margin: 0;">-<span id="LC1391" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">BAMPatternSource</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">get_or_store_orhaned_mate</span><span class="p">(</span><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;">buf_a</span><span class="p">,</span> <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;">buf_b</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">readi</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uint8_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">mate</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">mate_len</span><span class="p">)</span> <span class="p">{</span></span>
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1392
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<pre style="margin: 0;">-<span id="LC1392" 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;">read_name</span> <span class="o" style="font-weight: 600;">=</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1393" 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">
1393
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<td class="new_line diff-line-num old" data-linenumber="1390" 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="LC1393" class="line" lang="cpp"> <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="p">)(</span><span class="n" style="color: #333;">mate</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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1394
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<pre style="margin: 0;">-<span id="LC1394" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">i</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1395" 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">
1395
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<td class="new_line diff-line-num old" data-linenumber="1390" 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="LC1395" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">hash</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">hash_str</span><span class="p">(</span><span class="n" style="color: #333;">read_name</span><span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1396" 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">
1396
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<pre style="margin: 0;">-<span id="LC1396" class="line" lang="cpp"> <span class="n" style="color: #333;">orphan_mate_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">empty_slot</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="old_line diff-line-num old" data-linenumber="1397" 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">
1397
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<td class="new_line diff-line-num old" data-linenumber="1390" 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="LC1397" class="line" lang="cpp"></span>
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<td class="old_line diff-line-num old" data-linenumber="1398" 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">
1398
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<td class="new_line diff-line-num old" data-linenumber="1390" 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="LC1398" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">orphan_mates</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1399" 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">
1399
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<td class="new_line diff-line-num old" data-linenumber="1390" 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="LC1399" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">empty_slot</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">NULL</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">orphan_mates</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">empty</span><span class="p">())</span></span>
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1400
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<td class="new_line diff-line-num old" data-linenumber="1390" 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="LC1400" class="line" lang="cpp"> <span class="n" style="color: #333;">empty_slot</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">orphan_mates</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1401" 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">
1401
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<pre style="margin: 0;">-<span id="LC1401" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">orphan_mates</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">hash</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">hash</span><span class="p">)</span></span>
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1402
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<pre style="margin: 0;">-<span id="LC1402" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC1403" class="line" lang="cpp"> <span class="p">}</span></span>
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1404
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<pre style="margin: 0;">-<span id="LC1404" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">orphan_mates</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">())</span> <span class="p">{</span></span>
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1405
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<pre style="margin: 0;">-<span id="LC1405" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// vector is full</span></span>
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1406
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<pre style="margin: 0;">-<span id="LC1406" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">empty_slot</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="old_line diff-line-num old" data-linenumber="1407" 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">
1407
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<pre style="margin: 0;">-<span id="LC1407" class="line" lang="cpp"> <span class="n" style="color: #333;">orphan_mates</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">orphan_mate_t</span><span class="p">());</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1408" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1408
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<pre style="margin: 0;">-<span id="LC1408" class="line" lang="cpp"> <span class="n" style="color: #333;">empty_slot</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">orphan_mates</span><span class="p">.</span><span class="n" style="color: #333;">back</span><span class="p">();</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1409" 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">
1409
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<pre style="margin: 0;">-<span id="LC1409" class="line" lang="cpp"> <span class="p">}</span></span>
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1410
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<pre style="margin: 0;">-<span id="LC1410" class="line" lang="cpp"> <span class="n" style="color: #333;">empty_slot</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">hash</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">hash</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1411" 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">
1411
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<pre style="margin: 0;">-<span id="LC1411" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">empty_slot</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">cap</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">mate_len</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1412" 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">
1412
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<td class="new_line diff-line-num old" data-linenumber="1390" 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="LC1412" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">delete</span><span class="p">[]</span> <span class="n" style="color: #333;">empty_slot</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1413" 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">
1413
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<pre style="margin: 0;">-<span id="LC1413" class="line" lang="cpp"> <span class="n" style="color: #333;">empty_slot</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="old_line diff-line-num old" data-linenumber="1414" 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">
1414
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<pre style="margin: 0;">-<span id="LC1414" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1415" 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">
1415
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<pre style="margin: 0;">-<span id="LC1415" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">empty_slot</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 class="p">{</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1416" 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">
1416
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<td class="new_line diff-line-num old" data-linenumber="1390" 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="LC1416" class="line" lang="cpp"> <span class="n" style="color: #333;">empty_slot</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="k" style="font-weight: 600;">new</span> <span class="kt" style="color: #458; font-weight: 600;">uint8_t</span><span class="p">[</span><span class="n" style="color: #333;">mate_len</span><span class="p">];</span></span>
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1417
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<td class="new_line diff-line-num old" data-linenumber="1390" 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="LC1417" class="line" lang="cpp"> <span class="n" style="color: #333;">empty_slot</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">cap</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mate_len</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1418" 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">
1418
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<pre style="margin: 0;">-<span id="LC1418" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1419" 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">
1419
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<td class="new_line diff-line-num old" data-linenumber="1390" 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="LC1419" class="line" lang="cpp"> <span class="n" style="color: #333;">memcpy</span><span class="p">(</span><span class="n" style="color: #333;">empty_slot</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">data</span><span class="p">,</span> <span class="n" style="color: #333;">mate</span><span class="p">,</span> <span class="n" style="color: #333;">mate_len</span><span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1420" 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">
1420
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<pre style="margin: 0;">-<span id="LC1420" class="line" lang="cpp"> <span class="n" style="color: #333;">empty_slot</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">size</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mate_len</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1421" 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">
1421
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<td class="new_line diff-line-num old" data-linenumber="1390" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1421" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1422" 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">
1422
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<pre style="margin: 0;">-<span id="LC1422" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint8_t</span> <span class="n" style="color: #333;">flag</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1423" 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">
1423
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<pre style="margin: 0;">-<span id="LC1423" class="line" lang="cpp"> <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="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">buf_a</span><span class="p">[</span><span class="n" style="color: #333;">readi</span><span class="p">];</span></span>
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1424
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<pre style="margin: 0;">-<span id="LC1424" class="line" lang="cpp"> <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="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">buf_b</span><span class="p">[</span><span class="n" style="color: #333;">readi</span><span class="p">];</span></span>
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1425
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<td class="new_line diff-line-num old" data-linenumber="1390" 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="LC1425" class="line" lang="cpp"></span>
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<td class="old_line diff-line-num old" data-linenumber="1426" 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">
1426
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<pre style="margin: 0;">-<span id="LC1426" 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;">mate</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="old_line diff-line-num old" data-linenumber="1427" 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">
1427
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<pre style="margin: 0;">-<span id="LC1427" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</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="old_line diff-line-num old" data-linenumber="1428" 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">
1428
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<td class="new_line diff-line-num old" data-linenumber="1390" 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="LC1428" class="line" lang="cpp"> <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;">resize</span><span class="p">(</span><span class="n" style="color: #333;">mate_len</span><span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1429" 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">
1429
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<td class="new_line diff-line-num old" data-linenumber="1390" 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="LC1429" class="line" lang="cpp"> <span class="n" style="color: #333;">memcpy</span><span class="p">(</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;">wbuf</span><span class="p">(),</span> <span class="n" style="color: #333;">mate</span><span class="p">,</span> <span class="n" style="color: #333;">mate_len</span><span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1430" 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">
1430
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<td class="new_line diff-line-num old" data-linenumber="1390" 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="LC1430" class="line" lang="cpp"> <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;">resize</span><span class="p">(</span><span class="n" style="color: #333;">orphan_mates</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">size</span><span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1431" 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">
1431
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<td class="new_line diff-line-num old" data-linenumber="1390" 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="LC1431" class="line" lang="cpp"> <span class="n" style="color: #333;">memcpy</span><span class="p">(</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;">wbuf</span><span class="p">(),</span> <span class="n" style="color: #333;">orphan_mates</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">data</span><span class="p">,</span> <span class="n" style="color: #333;">orphan_mates</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">size</span><span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1432" 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">
1432
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<td class="new_line diff-line-num old" data-linenumber="1390" 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="LC1432" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1433" 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">
1433
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<td class="new_line diff-line-num old" data-linenumber="1390" 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="LC1433" class="line" lang="cpp"> <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;">resize</span><span class="p">(</span><span class="n" style="color: #333;">mate_len</span><span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1434" 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">
1434
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<td class="new_line diff-line-num old" data-linenumber="1390" 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="LC1434" class="line" lang="cpp"> <span class="n" style="color: #333;">memcpy</span><span class="p">(</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;">wbuf</span><span class="p">(),</span> <span class="n" style="color: #333;">mate</span><span class="p">,</span> <span class="n" style="color: #333;">mate_len</span><span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1435" 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">
1435
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<td class="new_line diff-line-num old" data-linenumber="1390" 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="LC1435" class="line" lang="cpp"> <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;">resize</span><span class="p">(</span><span class="n" style="color: #333;">orphan_mates</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">size</span><span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1436" 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">
1436
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<td class="new_line diff-line-num old" data-linenumber="1390" 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="LC1436" class="line" lang="cpp"> <span class="n" style="color: #333;">memcpy</span><span class="p">(</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;">wbuf</span><span class="p">(),</span> <span class="n" style="color: #333;">orphan_mates</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">data</span><span class="p">,</span> <span class="n" style="color: #333;">orphan_mates</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">size</span><span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1437" 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">
1437
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<td class="new_line diff-line-num old" data-linenumber="1390" 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="LC1437" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1438" 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">
1438
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<td class="new_line diff-line-num old" data-linenumber="1390" 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="LC1438" 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>
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<td class="old_line diff-line-num old" data-linenumber="1439" 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">
1439
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<pre style="margin: 0;">-<span id="LC1439" class="line" lang="cpp"> <span class="n" style="color: #333;">orphan_mates</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">reset</span><span class="p">();</span></span>
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1440
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<td class="new_line diff-line-num old" data-linenumber="1390" 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="LC1440" class="line" lang="cpp"> <span class="p">}</span></span>
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1441
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<pre style="margin: 0;">-<span id="LC1441" class="line" lang="cpp"><span class="p">}</span></span>
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1442
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<pre style="margin: 0;">-<span id="LC1442" class="line" lang="cpp"></span>
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1443
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1390
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<pre style="margin: 0;"> <span id="LC1390" class="line" lang="cpp"><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;">decompress_bgzf_block</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint8_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">dst</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">dst_len</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint8_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">src</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">src_len</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC1444" class="line" lang="cpp"> <span class="n" style="color: #333;">z_stream</span> <span class="n" style="color: #333;">strm</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC1445" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC1446" class="line" lang="cpp"> <span class="n" style="color: #333;">strm</span><span class="p">.</span><span class="n" style="color: #333;">zalloc</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Z_NULL</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC1447" class="line" lang="cpp"> <span class="n" style="color: #333;">strm</span><span class="p">.</span><span class="n" style="color: #333;">zfree</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Z_NULL</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC1448" class="line" lang="cpp"> <span class="n" style="color: #333;">strm</span><span class="p">.</span><span class="n" style="color: #333;">opaque</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Z_NULL</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC1391" class="line" lang="cpp"> <span class="n" style="color: #333;">stream</span><span class="p">.</span><span class="n" style="color: #333;">zalloc</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Z_NULL</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC1392" class="line" lang="cpp"> <span class="n" style="color: #333;">stream</span><span class="p">.</span><span class="n" style="color: #333;">zfree</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Z_NULL</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC1393" class="line" lang="cpp"> <span class="n" style="color: #333;">stream</span><span class="p">.</span><span class="n" style="color: #333;">opaque</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Z_NULL</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC1394" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC1450" class="line" lang="cpp"> <span class="n" style="color: #333;">strm</span><span class="p">.</span><span class="n" style="color: #333;">avail_in</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">src_len</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC1451" class="line" lang="cpp"> <span class="n" style="color: #333;">strm</span><span class="p">.</span><span class="n" style="color: #333;">next_in</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">src</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC1452" class="line" lang="cpp"> <span class="n" style="color: #333;">strm</span><span class="p">.</span><span class="n" style="color: #333;">avail_out</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dst_len</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC1453" class="line" lang="cpp"> <span class="n" style="color: #333;">strm</span><span class="p">.</span><span class="n" style="color: #333;">next_out</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dst</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC1395" class="line" lang="cpp"> <span class="n" style="color: #333;">str<span class="idiff left right">ea</span>m</span><span class="p">.</span><span class="n" style="color: #333;">avail_in</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">src_len</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC1396" class="line" lang="cpp"> <span class="n" style="color: #333;">str<span class="idiff left right">ea</span>m</span><span class="p">.</span><span class="n" style="color: #333;">next_in</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">src</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC1397" class="line" lang="cpp"> <span class="n" style="color: #333;">str<span class="idiff left right">ea</span>m</span><span class="p">.</span><span class="n" style="color: #333;">avail_out</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dst_len</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC1398" class="line" lang="cpp"> <span class="n" style="color: #333;">str<span class="idiff left right">ea</span>m</span><span class="p">.</span><span class="n" style="color: #333;">next_out</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dst</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC1399" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC1455" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ret</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">inflateInit2</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">strm</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">8</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC1400" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ret</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">inflateInit2</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">str<span class="idiff left right">ea</span>m</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">8</span><span class="p">);</span></span>
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1456
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1401
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<pre style="margin: 0;"> <span id="LC1401" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">ret</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">Z_OK</span><span class="p">)</span> <span class="p">{</span></span>
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1457
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1402
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<pre style="margin: 0;"> <span id="LC1402" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">ret</span><span class="p">;</span></span>
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1458
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1403
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<pre style="margin: 0;"> <span id="LC1403" class="line" lang="cpp"> <span class="p">}</span></span>
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1459
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1404
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<pre style="margin: 0;"> <span id="LC1404" class="line" lang="cpp"></span>
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1460
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<pre style="margin: 0;">-<span id="LC1460" class="line" lang="cpp"> <span class="n" style="color: #333;">ret</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">inflate</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">strm</span><span class="p">,</span> <span class="n" style="color: #333;">Z_FINISH</span><span class="p">);</span></span>
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1405
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<pre style="margin: 0;">+<span id="LC1405" class="line" lang="cpp"> <span class="n" style="color: #333;">ret</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">inflate</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">str<span class="idiff left right">ea</span>m</span><span class="p">,</span> <span class="n" style="color: #333;">Z_FINISH</span><span class="p">);</span></span>
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1461
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1406
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<pre style="margin: 0;"> <span id="LC1406" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">ret</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">Z_STREAM_END</span><span class="p">)</span> <span class="p">{</span></span>
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1462
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1407
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<pre style="margin: 0;"> <span id="LC1407" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">ret</span><span class="p">;</span></span>
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1463
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1408
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<pre style="margin: 0;"> <span id="LC1408" class="line" lang="cpp"> <span class="p">}</span></span>
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1464
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1409
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<pre style="margin: 0;"> <span id="LC1409" class="line" lang="cpp"></span>
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1465
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<pre style="margin: 0;">-<span id="LC1465" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">inflate<span class="idiff left right">End</span></span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">strm</span><span class="p">);</span></span>
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1410
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<pre style="margin: 0;">+<span id="LC1410" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">inflate<span class="idiff left">Reset</span></span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">str<span class="idiff right">ea</span>m</span><span class="p">);</span></span>
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1466
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1411
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<pre style="margin: 0;"> <span id="LC1411" class="line" lang="cpp"><span class="p">}</span></span>
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1412
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<pre style="margin: 0;"> <span id="LC1412" class="line" lang="cpp"></span>
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1413
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<pre style="margin: 0;"> <span id="LC1413" 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="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -826,28 +826,6 @@ class BAMPatternSource : public CFilePatternSource {</td>
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<pre style="margin: 0;"> <span id="LC826" class="line" lang="cpp"> <span class="n" style="color: #333;">ftr_t</span> <span class="n" style="color: #333;">ftr</span><span class="p">;</span></span>
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827
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<pre style="margin: 0;"> <span id="LC827" class="line" lang="cpp"> <span class="p">};</span></span>
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828
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<pre style="margin: 0;"> <span id="LC828" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC829" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">orphan_mate_t</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC830" class="line" lang="cpp"> <span class="n" style="color: #333;">orphan_mate_t</span><span class="p">()</span> <span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;">-<span id="LC831" class="line" lang="cpp"> <span class="n" style="color: #333;">data</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="LC832" class="line" lang="cpp"> <span class="n" style="color: #333;">size</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">),</span></span>
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<pre style="margin: 0;">-<span id="LC833" class="line" lang="cpp"> <span class="n" style="color: #333;">cap</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">),</span></span>
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<pre style="margin: 0;">-<span id="LC834" class="line" lang="cpp"> <span class="n" style="color: #333;">hash</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{}</span></span>
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<pre style="margin: 0;">-<span id="LC835" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC836" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">reset</span><span class="p">()</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC837" class="line" lang="cpp"> <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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<pre style="margin: 0;">-<span id="LC838" class="line" lang="cpp"> <span class="n" style="color: #333;">hash</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="LC839" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC840" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC841" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">empty</span><span class="p">()</span> <span class="k" style="font-weight: 600;">const</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC842" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</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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<pre style="margin: 0;">-<span id="LC843" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC844" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC845" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint8_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">data</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC846" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint16_t</span> <span class="n" style="color: #333;">size</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC847" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint16_t</span> <span class="n" style="color: #333;">cap</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC848" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">hash</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC849" class="line" lang="cpp"> <span class="p">};</span></span>
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<pre style="margin: 0;">-<span id="LC850" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC829" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">BAMField</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC830" class="line" lang="cpp"> <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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<pre style="margin: 0;"> <span id="LC831" class="line" lang="cpp"> <span class="n" style="color: #333;">refID</span><span class="p">,</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="872" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -872,15 +850,15 @@ public:</td>
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<pre style="margin: 0;"> <span id="LC850" class="line" lang="cpp"> <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="LC851" class="line" lang="cpp"> <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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852
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<pre style="margin: 0;"> <span id="LC852" class="line" lang="cpp"> <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>
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<pre style="margin: 0;">-<span id="LC875" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">bam_batches_</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">p</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">nthreads</span></span><span class="p">),</span></span>
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<pre style="margin: 0;">-<span id="LC876" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">bam_batch_indexes_</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">p</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">nthreads</span></span><span class="p">),</span></span>
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877
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<pre style="margin: 0;">-<span id="LC877" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">orphan_mates</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">p</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">nthreads</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">2</span></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="n" style="color: #333;"><span class="idiff left">orphan_mates_mutex_</span></span><span class="p"><span class="idiff right">(),</span></span></span>
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<pre style="margin: 0;">-<span id="LC879" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">pp_</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">p</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff right"> </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="c1" style="color: #998; font-style: italic;"><span class="idiff left right">// uncompressed size of BGZF block is limited to 2**16 bytes</span></span></span>
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881
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<pre style="margin: 0;">-<span id="LC881" class="line" lang="cpp"> <span class="k" style="font-weight: 600;"><span class="idiff left">for</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">size_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">i</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">0</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">i</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">bam_batches_</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">size</span></span><span class="p"><span class="idiff">();</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">++</span></span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="p"><span class="idiff right">{</span></span></span>
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882
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<pre style="margin: 0;">-<span id="LC882" class="line" lang="cpp"> <span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">bam_batches_</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">reserve</span></span><span class="p"><span class="idiff">(</span></span><span class="mi" style="color: #099;"><span class="idiff">1</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">16</span></span><span class="p"><span class="idiff right">)</span>;</span></span>
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883
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<pre style="margin: 0;">-<span id="LC883" class="line" lang="cpp"> <span class="p"><span class="idiff left right">}</span></span></span>
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853
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<pre style="margin: 0;">+<span id="LC853" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">alignment_batch</span></span><span class="p"><span class="idiff">(</span></span><span class="mi" style="color: #099;"><span class="idiff right">0</span></span><span class="p">),</span></span>
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854
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<pre style="margin: 0;">+<span id="LC854" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">alignment_offset</span></span><span class="p"><span class="idiff">(</span></span><span class="mi" style="color: #099;"><span class="idiff right">0</span></span><span class="p">),</span></span>
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855
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<pre style="margin: 0;">+<span id="LC855" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">delta_</span></span><span class="p"><span class="idiff">(</span></span><span class="mi" style="color: #099;"><span class="idiff right">0</span></span><span class="p">),</span></span>
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856
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<pre style="margin: 0;">+<span id="LC856" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">pp_</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">p</span></span><span class="p"><span class="idiff right">)</span></span></span>
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857
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<pre style="margin: 0;">+<span id="LC857" class="line" lang="cpp"> <span class="p">{</span></span>
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858
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<pre style="margin: 0;">+<span id="LC858" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">stream</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">zalloc</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">Z_NULL</span></span><span class="p"><span class="idiff right">;</span></span></span>
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859
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<pre style="margin: 0;">+<span id="LC859" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">stream</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">zfree</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">Z_NULL</span></span><span class="p"><span class="idiff right">;</span></span></span>
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860
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<pre style="margin: 0;">+<span id="LC860" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">stream</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">opaque</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 right">Z_NULL</span></span><span class="p">;</span></span>
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861
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<pre style="margin: 0;">+<span id="LC861" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">alignment_batch</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">reserve</span></span><span class="p"><span class="idiff">(</span></span><span class="mi" style="color: #099;"><span class="idiff">1</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">16</span></span><span class="p"><span class="idiff right">);</span></span></span>
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<pre style="margin: 0;"> <span id="LC862" class="line" lang="cpp"> <span class="p">}</span></span>
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863
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<pre style="margin: 0;"> <span id="LC863" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC864" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">virtual</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">reset</span><span class="p">()</span> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="872" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -894,11 +872,6 @@ public:</td>
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<pre style="margin: 0;"> <span id="LC872" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">virtual</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">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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873
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<pre style="margin: 0;"> <span id="LC873" class="line" lang="cpp"></span>
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874
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<pre style="margin: 0;"> <span id="LC874" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">~</span><span class="n" style="color: #333;">BAMPatternSource</span><span class="p">()</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC897" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">orphan_mates</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC898" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">orphan_mates</span><span class="p">[</span><span class="n" style="color: #333;">i</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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<pre style="margin: 0;">-<span id="LC899" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">delete</span><span class="p">[]</span> <span class="n" style="color: #333;">orphan_mates</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">data</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC900" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC901" 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>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="924" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -924,18 +897,14 @@ private:</td>
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<pre style="margin: 0;"> <span id="LC897" class="line" lang="cpp"></span>
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898
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<pre style="margin: 0;"> <span id="LC898" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">decompress_bgzf_block</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint8_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">dst</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">dst_len</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint8_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">src</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">src_len</span><span class="p">);</span></span>
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899
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<pre style="margin: 0;"> <span id="LC899" class="line" lang="cpp"> <span class="n" style="color: #333;">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;">get_alignments</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="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="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">readi</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">lock</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC927" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">store_orphan_mate</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uint8_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">read</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">read_len</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC928" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">get_orphaned_pairs</span><span class="p">(</span><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;">buf_a</span><span class="p">,</span> <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;">buf_b</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">max_buf</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">readi</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC929" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">get_or_store_orhaned_mate</span><span class="p">(</span><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;">buf_a</span><span class="p">,</span> <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;">buf_b</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">readi</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uint8_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">mate</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">mate_len</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC930" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">get_matching_read</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uint8_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">rec</span><span class="p">);</span></span>
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931
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900
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<pre style="margin: 0;"> <span id="LC900" class="line" lang="cpp"></span>
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932
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<pre style="margin: 0;">-<span id="LC932" class="line" lang="cpp"><span class="idiff left right"> </span><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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901
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<pre style="margin: 0;">+<span id="LC901" class="line" lang="cpp"><span class="idiff left right"> </span><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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933
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902
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<pre style="margin: 0;"> <span id="LC902" 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;">uint8_t</span> <span class="n" style="color: #333;">EOF_MARKER</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>
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935
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<pre style="margin: 0;">-<span id="LC935" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;"><span class="idiff left">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">vector</span></span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint8_t</span></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="n" style="color: #333;"><span class="idiff">bam</span>_batch<span class="idiff right">es_</span></span><span class="p">;</span></span>
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936
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<pre style="margin: 0;">-<span id="LC936" class="line" lang="cpp"> <span class="n" style="color: #333;">s<span class="idiff left">td</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">vector</span></span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">size_t</span></span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">bam_batch_indexes_</span></span><span class="p">;</span></span>
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937
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<pre style="margin: 0;">-<span id="LC937" class="line" lang="cpp"> <span class="n" style="color: #333;">s<span class="idiff left">td</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">vector</span></span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="n" style="color: #333;"><span class="idiff">orphan_mate_t</span></span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">orphan_mates</span></span><span class="p">;</span></span>
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938
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<pre style="margin: 0;">-<span id="LC938" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">MUTEX_T</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">orphan_mates_mutex_</span></span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC904" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">uint8_t</span></span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">alignment</span>_batch</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC905" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">s<span class="idiff left">ize_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">alignment_offset</span></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="kt" style="color: #458; font-weight: 600;">s<span class="idiff left">ize_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">delta_</span></span><span class="p">;</span></span>
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907
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<pre style="margin: 0;">+<span id="LC907" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">z_stream</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">stream</span></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>
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940
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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;">PatternParams</span> <span class="n" style="color: #333;">pp_</span><span class="p">;</span></span>
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941
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<pre style="margin: 0;"> <span id="LC910" class="line" lang="cpp"><span class="p">};</span></span>
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<a href="https://salsa.debian.org/med-team/bowtie2/-/commit/cf277464ee949fe563ca814a827b2387be02dbd1#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">@@ -275,9 +275,7 @@ fastaRefReadSizes(</td>
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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="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="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;">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="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="LC280" class="line" lang="cpp"> <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;">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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<a href="https://salsa.debian.org/med-team/bowtie2/-/commit/cf277464ee949fe563ca814a827b2387be02dbd1#c1e31d3892dc5f604d89ce46343574400583f46f"><strong>reference.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">@@ -595,8 +595,8 @@ BitPairReference::szsFromFasta(</td>
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<pre style="margin: 0;"> <span id="LC595" class="line" lang="cpp"> <span class="n" style="color: #333;">RefReadInParams</span> <span class="n" style="color: #333;">parms</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">refparams</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC596" class="line" lang="cpp"> <span class="n" style="color: #333;">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;">size_t</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;">sztot</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC597" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">outfile</span><span class="p">.</span><span class="n" style="color: #333;">empty</span><span class="p">())</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC598" class="line" lang="cpp"> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">file3</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">outfile</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">".3."</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">gEbwt_ext</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC599" class="line" lang="cpp"> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">file4</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">outfile</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">".4."</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">gEbwt_ext</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC598" class="line" lang="cpp"> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">file3</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">outfile</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">".3."</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">gEbwt_ext</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">".tmp"</span></span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC599" class="line" lang="cpp"> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">file4</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">outfile</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">".4."</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">gEbwt_ext</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">".tmp"</span></span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC600" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Open output stream for the '.3.gEbwt_ext' file which will</span></span>
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<pre style="margin: 0;"> <span id="LC601" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// hold the size records.</span></span>
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<pre style="margin: 0;"> <span id="LC602" class="line" lang="cpp"> <span class="n" style="color: #333;">ofstream</span> <span class="n" style="color: #333;">fout3</span><span class="p">(</span><span class="n" style="color: #333;">file3</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">(),</span> <span class="n" style="color: #333;">ios</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">binary</span><span class="p">);</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -59,7 +59,7 @@ void SamConfig::printHeader(</td>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">printSq</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">printPg</span><span class="p">)</span> <span class="k" style="font-weight: 600;">const</span></span>
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="cpp"><span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">printHd</span><span class="p">)</span> <span class="n" style="color: #333;">printHdLine</span><span class="p">(</span><span class="n" style="color: #333;">o</span><span class="p">,</span> <span class="s" style="color: #d14;">"1.<span class="idiff left right">0</span>"</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">printHd</span><span class="p">)</span> <span class="n" style="color: #333;">printHdLine</span><span class="p">(</span><span class="n" style="color: #333;">o</span><span class="p">,</span> <span class="s" style="color: #d14;">"1.<span class="idiff left right">5</span>"</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">printSq</span><span class="p">)</span> <span class="n" style="color: #333;">printSqLines</span><span class="p">(</span><span class="n" style="color: #333;">o</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC64" 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;">rgid</span><span class="p">.</span><span class="n" style="color: #333;">empty</span><span class="p">())</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC65" 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="s" style="color: #d14;">"@RG"</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">@@ -76,7 +76,7 @@ void SamConfig::printHeader(</td>
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<pre style="margin: 0;"> <span id="LC76" 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;">printHdLine</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="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">samver</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="LC77" 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="s" style="color: #d14;">"@HD</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">VN:"</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;">o</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">samver</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC79" class="line" lang="cpp"> <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">SO:unsorted</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC79" 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="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">SO:unsorted</span><span class="se" style="color: #d14;">\<span class="idiff left">t</span></span><span class="s" style="color: #d14;"><span class="idiff">GO:query</span></span><span class="se" style="color: #d14;"><span class="idiff right">\</span>n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="cpp"><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">@@ -526,11 +526,6 @@ void SamConfig::printAlignedOptFlags(</td>
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<pre style="margin: 0;"> <span id="LC526" 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="s" style="color: #d14;">"ZI:i:"</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC527" 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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<pre style="margin: 0;"> <span id="LC528" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC529" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">print_xr_</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC530" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Original read string</span></span>
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<pre style="margin: 0;">-<span id="LC531" 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="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC532" 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="LC533" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC529" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">print_zt_</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC530" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// ZT:Z: Extra features for MAPQ estimation</span></span>
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<pre style="margin: 0;"> <span id="LC531" class="line" lang="cpp"> <span class="n" style="color: #333;">WRITE_SEP</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">@@ -881,18 +876,13 @@ void SamConfig::printEmptyOptFlags(</td>
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<pre style="margin: 0;"> <span id="LC876" 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="s" style="color: #d14;">"ZI:i:"</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC877" 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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<pre style="margin: 0;"> <span id="LC878" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC884" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">print_xr_</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC885" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Original read string</span></span>
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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="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC887" 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="LC888" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC879" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC880" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC881" 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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892
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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;">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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893
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<pre style="margin: 0;">-<span id="LC893" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">char</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">buf</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">1024</span></span><span class="p"><span class="idiff right">]</span>;</span></span>
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883
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<pre style="margin: 0;">+<span id="LC883" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">uint32_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">count</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>
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894
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884
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<pre style="margin: 0;"> <span id="LC884" 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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895
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<pre style="margin: 0;">-<span id="LC895" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right">in</span>t</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">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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885
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<pre style="margin: 0;">+<span id="LC885" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right">size_</span>t</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">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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896
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886
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<pre style="margin: 0;"> <span id="LC886" 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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897
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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;">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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898
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888
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<pre style="margin: 0;"> <span id="LC888" 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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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="900" style="width: 35px; color: rgba(0,0,0,0.3); 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="890" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -900,78 +890,64 @@ void SamConfig::printPreservedOptFlags(BTString& o, const Read& rd) const {</td>
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900
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890
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<pre style="margin: 0;"> <span id="LC890" 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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901
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891
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<pre style="margin: 0;"> <span id="LC891" class="line" lang="cpp"> <span class="n" style="color: #333;">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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902
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892
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<pre style="margin: 0;"> <span id="LC892" class="line" lang="cpp"> <span class="n" style="color: #333;">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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903
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<pre style="margin: 0;">-<span id="LC903" 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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904
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<pre style="margin: 0;">-<span id="LC904" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">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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905
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<pre style="margin: 0;">-<span id="LC905" 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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906
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<pre style="margin: 0;">-<span id="LC906" 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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907
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<pre style="margin: 0;">-<span id="LC907" 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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908
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<pre style="margin: 0;">-<span id="LC908" 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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893
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<pre style="margin: 0;">+<span id="LC893" 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;">'B'</span><span class="p">)</span> <span class="p">{</span></span>
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894
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<pre style="margin: 0;">+<span id="LC894" class="line" lang="cpp"> <span class="n" style="color: #333;">i</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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895
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<pre style="margin: 0;">+<span id="LC895" 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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896
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<pre style="margin: 0;">+<span id="LC896" 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;">1</span><span class="p">;</span></span>
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897
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<pre style="margin: 0;">+<span id="LC897" class="line" lang="cpp"> <span class="n" style="color: #333;">memcpy</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">count</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;">count</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="n" style="color: #333;">count</span><span class="p">);</span></span>
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899
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<pre style="margin: 0;">+<span id="LC899" class="line" lang="cpp"> <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="s" style="color: #d14;">":B:"</span><span class="p">);</span></span>
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909
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900
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<pre style="margin: 0;"> <span id="LC900" class="line" lang="cpp"> <span class="n" style="color: #333;">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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910
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<pre style="margin: 0;">-<span id="LC910" class="line" lang="cpp"> <span class="p">}</span></span>
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911
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<pre style="margin: 0;">-<span id="LC911" class="line" lang="cpp"> <span class="n" style="color: #333;">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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912
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<pre style="margin: 0;">-<span id="LC912" 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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901
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<pre style="margin: 0;">+<span id="LC901" 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="s" style="color: #d14;">","</span><span class="p">);</span></span>
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902
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<pre style="margin: 0;">+<span id="LC902" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</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;">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="new_line diff-line-num new" 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="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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905
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<pre style="margin: 0;">+<span id="LC905" 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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906
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<pre style="margin: 0;">+<span id="LC906" 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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907
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<pre style="margin: 0;">+<span id="LC907" 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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908
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<pre style="margin: 0;">+<span id="LC908" 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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909
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<pre style="margin: 0;">+<span id="LC909" 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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910
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<pre style="margin: 0;">+<span id="LC910" class="line" lang="cpp"> <span class="p">}</span></span>
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911
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<pre style="margin: 0;">+<span id="LC911" class="line" lang="cpp"> <span class="n" style="color: #333;">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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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="sc" style="color: #d14;">':'</span><span class="p">);</span></span>
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913
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<pre style="margin: 0;">+<span id="LC913" class="line" lang="cpp"> <span class="p">}</span></span>
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913
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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;">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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914
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<td class="new_line diff-line-num old" data-linenumber="915" 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="LC914" 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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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;">char</span> <span class="n" style="color: #333;">A_val</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="916" 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">
916
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<td class="new_line diff-line-num old" data-linenumber="915" 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="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;">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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917
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<td class="new_line diff-line-num old" data-linenumber="915" 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="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;">A_val</span><span class="p">);</span></span>
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918
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<td class="new_line diff-line-num old" data-linenumber="915" 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="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;">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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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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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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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;">'c'</span><span class="p">:</span></span>
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<td class="old_line diff-line-num old" data-linenumber="922" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
922
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<pre style="margin: 0;">-<span id="LC922" class="line" lang="cpp"> <span class="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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<td class="old_line diff-line-num old" data-linenumber="923" 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">
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;">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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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;">c_val</span><span class="p">);</span></span>
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925
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<td class="new_line diff-line-num old" data-linenumber="915" 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="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;">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="old_line diff-line-num old" data-linenumber="926" 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">
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>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="927" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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="old_line diff-line-num old" data-linenumber="928" 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">
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;">'C'</span><span class="p">:</span></span>
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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;">uint8_t</span> <span class="n" style="color: #333;">C_val</span><span class="p">;</span></span>
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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;">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>
</pre>
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931
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<pre style="margin: 0;">-<span id="LC931" class="line" lang="cpp"> <span class="n" style="color: #333;">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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932
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<td class="new_line diff-line-num old" data-linenumber="915" 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="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;">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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933
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<td class="new_line diff-line-num old" data-linenumber="915" 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="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>
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<td class="old_line diff-line-num old" data-linenumber="934" 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">
934
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<td class="new_line diff-line-num old" data-linenumber="915" 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="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="old_line diff-line-num old" data-linenumber="935" 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">
935
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<td class="new_line diff-line-num old" data-linenumber="915" 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="LC935" 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="old_line diff-line-num old" data-linenumber="936" 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">
936
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<td class="new_line diff-line-num old" data-linenumber="915" 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="LC936" 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="old_line diff-line-num old" data-linenumber="937" 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">
937
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<td class="new_line diff-line-num old" data-linenumber="915" 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="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;">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="old_line diff-line-num old" data-linenumber="938" 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">
938
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<td class="new_line diff-line-num old" data-linenumber="915" 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="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;">s_val</span><span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="939" 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">
939
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<td class="new_line diff-line-num old" data-linenumber="915" 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="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;">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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940
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<td class="new_line diff-line-num old" data-linenumber="915" 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="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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<td class="old_line diff-line-num old" data-linenumber="941" 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">
941
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<td class="new_line diff-line-num old" data-linenumber="915" 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="LC941" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="942" 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">
942
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<td class="new_line diff-line-num old" data-linenumber="915" 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="LC942" 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="old_line diff-line-num old" data-linenumber="943" 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">
943
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<td class="new_line diff-line-num old" data-linenumber="915" 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="LC943" 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="old_line diff-line-num old" data-linenumber="944" 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">
944
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<td class="new_line diff-line-num old" data-linenumber="915" 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="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;">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>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="945" 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">
945
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<td class="new_line diff-line-num old" data-linenumber="915" 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="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;">S_val</span><span class="p">);</span></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="946" 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">
946
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<td class="new_line diff-line-num old" data-linenumber="915" 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="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;">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="old_line diff-line-num old" data-linenumber="947" 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">
947
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<td class="new_line diff-line-num old" data-linenumber="915" 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="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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<td class="old_line diff-line-num old" data-linenumber="948" 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">
948
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<td class="new_line diff-line-num old" data-linenumber="915" 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="LC948" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="949" 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">
949
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<td class="new_line diff-line-num old" data-linenumber="915" 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="LC949" 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="old_line diff-line-num old" data-linenumber="950" 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">
950
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<td class="new_line diff-line-num old" data-linenumber="915" 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="LC950" 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="old_line diff-line-num old" data-linenumber="951" 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">
951
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<td class="new_line diff-line-num old" data-linenumber="915" 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="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;">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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952
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<pre style="margin: 0;">-<span id="LC952" 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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<pre style="margin: 0;">-<span id="LC953" 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>
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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;">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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955
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<pre style="margin: 0;">-<span id="LC955" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</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="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'I'</span><span class="p">:</span></span>
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957
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<pre style="margin: 0;">-<span id="LC957" class="line" lang="cpp"> <span class="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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958
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<pre style="margin: 0;">-<span id="LC958" 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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959
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<pre style="margin: 0;">-<span id="LC959" 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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960
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<td class="new_line diff-line-num old" data-linenumber="915" 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="LC960" 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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961
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<pre style="margin: 0;">-<span id="LC961" 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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962
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<pre style="margin: 0;">-<span id="LC962" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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963
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<pre style="margin: 0;">-<span id="LC963" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'Z'</span><span class="p">:</span></span>
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964
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<td class="new_line diff-line-num old" data-linenumber="915" 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="LC964" 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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965
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<td class="new_line diff-line-num old" data-linenumber="915" 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="LC965" 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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966
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<pre style="margin: 0;">-<span id="LC966" 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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967
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<pre style="margin: 0;">-<span id="LC967" 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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968
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<td class="new_line diff-line-num old" data-linenumber="915" 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="LC968" 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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969
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<pre style="margin: 0;">-<span id="LC969" 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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970
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<td class="new_line diff-line-num old" data-linenumber="915" 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="LC970" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="new_line diff-line-num new" 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="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="new_line diff-line-num new" 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;">readTagVal</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;">o</span><span class="p">,</span> <span class="n" style="color: #333;">b</span><span class="p">,</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">count</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="917" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
917
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<pre style="margin: 0;">+<span id="LC917" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="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="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="new_line diff-line-num new" 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;">readTagVal</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;">o</span><span class="p">,</span> <span class="n" style="color: #333;">b</span><span class="p">,</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">count</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" 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="new_line diff-line-num new" 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;">'C'</span><span class="p">:</span></span>
</pre>
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<td class="new_line diff-line-num new" data-linenumber="922" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
922
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<pre style="margin: 0;">+<span id="LC922" class="line" lang="cpp"> <span class="n" style="color: #333;">readTagVal</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;">o</span><span class="p">,</span> <span class="n" style="color: #333;">b</span><span class="p">,</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">count</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" 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="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="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="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'s'</span><span class="p">:</span></span>
</pre>
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<td class="new_line diff-line-num new" 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;">readTagVal</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;">o</span><span class="p">,</span> <span class="n" style="color: #333;">b</span><span class="p">,</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">count</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" 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="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="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;">case</span> <span class="sc" style="color: #d14;">'S'</span><span class="p">:</span></span>
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<td class="new_line diff-line-num new" data-linenumber="928" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
928
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<pre style="margin: 0;">+<span id="LC928" class="line" lang="cpp"> <span class="n" style="color: #333;">readTagVal</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;">o</span><span class="p">,</span> <span class="n" style="color: #333;">b</span><span class="p">,</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">count</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" 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="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
</pre>
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<td class="new_line diff-line-num new" 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="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="new_line diff-line-num new" 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;">readTagVal</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;">o</span><span class="p">,</span> <span class="n" style="color: #333;">b</span><span class="p">,</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">count</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" 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="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="971" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="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="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="old_line diff-line-num new" data-linenumber="971" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="934" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
934
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<pre style="margin: 0;">+<span id="LC934" class="line" lang="cpp"> <span class="n" style="color: #333;">readTagVal</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;">o</span><span class="p">,</span> <span class="n" style="color: #333;">b</span><span class="p">,</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">count</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" 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;">break</span><span class="p">;</span></span>
</pre>
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<td class="new_line diff-line-num new" 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="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'f'</span><span class="p">:</span></span>
</pre>
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937
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<pre style="margin: 0;">+<span id="LC937" class="line" lang="cpp"> <span class="n" style="color: #333;">readTagVal</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">float</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="n" style="color: #333;">o</span><span class="p">,</span> <span class="n" style="color: #333;">b</span><span class="p">,</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">count</span><span class="p">);</span></span>
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938
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<pre style="margin: 0;">+<span id="LC938" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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939
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<pre style="margin: 0;">+<span id="LC939" 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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940
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<pre style="margin: 0;">+<span id="LC940" 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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941
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<pre style="margin: 0;">+<span id="LC941" 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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942
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<pre style="margin: 0;">+<span id="LC942" 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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943
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<pre style="margin: 0;">+<span id="LC943" 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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971
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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;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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972
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<pre style="margin: 0;">-<span id="LC972" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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973
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<pre style="margin: 0;">-<span id="LC973" class="line" lang="cpp"> <span class="nl">default:</span></span>
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974
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<pre style="margin: 0;">-<span id="LC974" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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945
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<pre style="margin: 0;">+<span id="LC945" class="line" lang="cpp"> <span class="n" style="color: #333;">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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946
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<pre style="margin: 0;">+<span id="LC946" class="line" lang="cpp"> <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;">i</span><span class="o" style="font-weight: 600;">++</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="nl">default:</span></span>
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950
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<pre style="margin: 0;">+<span id="LC950" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</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="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="p">}</span></span>
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977
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953
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<pre style="margin: 0;"> <span id="LC953" class="line" lang="cpp"> <span class="p">}</span></span>
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<li id="7398ca21ea2a2c7a38ca176ea1edaeb67b9ca8c0">
<a href="https://salsa.debian.org/med-team/bowtie2/-/commit/cf277464ee949fe563ca814a827b2387be02dbd1#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">@@ -21,6 +21,7 @@</td>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#define SAM_H_</span></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="cpp"></span>
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23
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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 <string></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 <vector></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 "ds.h"</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 "read.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 "util.h"</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">@@ -328,6 +329,22 @@ public:</td>
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<pre style="margin: 0;"> <span id="LC329" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC330" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC331" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC332" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">template</span><span class="o" style="font-weight: 600;"><</span><span class="k" style="font-weight: 600;">typename</span> <span class="nc" style="color: #458; font-weight: 600;">T</span><span class="p">></span></span>
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<pre style="margin: 0;">+<span id="LC333" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">readTagVal</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="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="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;">offset</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">count</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC334" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">T</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">val</span><span class="p">(</span><span class="n" style="color: #333;">count</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC335" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC336" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC337" class="line" lang="cpp"> <span class="n" style="color: #333;">memcpy</span><span class="p">(</span><span class="n" style="color: #333;">val</span><span class="p">.</span><span class="n" style="color: #333;">data</span><span class="p">(),</span> <span class="n" style="color: #333;">data</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">offset</span><span class="p">,</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">T</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">count</span><span class="p">);</span></span>
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338
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<pre style="margin: 0;">+<span id="LC338" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">do</span> <span class="p">{</span></span>
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339
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<pre style="margin: 0;">+<span id="LC339" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">str</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">to_string</span><span class="p">(</span><span class="n" style="color: #333;">val</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]);</span></span>
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340
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<pre style="margin: 0;">+<span id="LC340" 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;">str</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">(),</span> <span class="n" style="color: #333;">str</span><span class="p">.</span><span class="n" style="color: #333;">length</span><span class="p">());</span></span>
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341
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<pre style="margin: 0;">+<span id="LC341" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="p">(</span><span class="n" style="color: #333;">count</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">))</span></span>
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342
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<pre style="margin: 0;">+<span id="LC342" 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="s" style="color: #d14;">","</span><span class="p">);</span></span>
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343
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<pre style="margin: 0;">+<span id="LC343" class="line" lang="cpp"> <span class="p">}</span> <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;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">count</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC344" class="line" lang="cpp"> <span class="n" style="color: #333;">offset</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;">T</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">count</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC345" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC348" 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="LC349" class="line" lang="cpp"><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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<pre style="margin: 0;"> <span id="LC350" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * that:</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">@@ -343,6 +360,10 @@ public:</td>
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<pre style="margin: 0;"> <span id="LC360" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">noUnal_</span><span class="p">;</span></span>
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361
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<pre style="margin: 0;"> <span id="LC361" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC362" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC363" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">passthrough</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="LC364" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">print_xr_</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC365" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC366" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC367" class="line" lang="cpp"><span class="nl">protected:</span></span>
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<pre style="margin: 0;"> <span id="LC368" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC369" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">truncQname_</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// truncate QNAME to 255 chars?</span></span>
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<a href="https://salsa.debian.org/med-team/bowtie2/-/commit/cf277464ee949fe563ca814a827b2387be02dbd1#3ec76e53f41bf5d12b7091741f12b8f2960bea2f"><strong>threadpool.h</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#ifndef _THREAD_POOL_H_</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#define _THREAD_POOL_H_</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <atomic></span></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <condition_variable></span></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <functional></span></span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <future></span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <iostream></span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <memory></span></span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <map></span></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <mutex></span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <queue></span></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <thread></span></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <vector></span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="cpp"></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="cpp"><span class="k" style="font-weight: 600;">template</span><span class="o" style="font-weight: 600;"><</span><span class="k" style="font-weight: 600;">typename</span> <span class="nc" style="color: #458; font-weight: 600;">T</span><span class="p">></span></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="cpp"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">threadsafe_queue</span> <span class="p">{</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="cpp"><span class="nl">private:</span></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">mutable</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">mutex</span> <span class="n" style="color: #333;">mut</span><span class="p">;</span></span>
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20
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<pre style="margin: 0;">+<span id="LC20" 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;">queue</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">T</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">data_queue</span><span class="p">;</span></span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="cpp"></span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="cpp"><span class="nl">public:</span></span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="cpp"> <span class="n" style="color: #333;">threadsafe_queue</span><span class="p">()</span> <span class="p">{}</span></span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="cpp"></span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">push</span><span class="p">(</span><span class="n" style="color: #333;">T</span> <span class="o" style="font-weight: 600;">&&</span><span class="n" style="color: #333;">new_value</span><span class="p">)</span> <span class="p">{</span></span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">lock_guard</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">mutex</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">lk</span><span class="p">(</span><span class="n" style="color: #333;">mut</span><span class="p">);</span></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="cpp"> <span class="n" style="color: #333;">data_queue</span><span class="p">.</span><span class="n" style="color: #333;">emplace</span><span class="p">(</span><span class="n" style="color: #333;">new_value</span><span class="p">);</span></span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="cpp"> <span class="p">}</span></span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">try_pop</span><span class="p">(</span><span class="n" style="color: #333;">T</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">value</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">lock_guard</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">mutex</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">lk</span><span class="p">(</span><span class="n" style="color: #333;">mut</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">data_queue</span><span class="p">.</span><span class="n" style="color: #333;">empty</span><span class="p">())</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">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="LC34" class="line" lang="cpp"> <span class="n" style="color: #333;">value</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">move</span><span class="p">(</span><span class="n" style="color: #333;">data_queue</span><span class="p">.</span><span class="n" style="color: #333;">front</span><span class="p">());</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="cpp"> <span class="n" style="color: #333;">data_queue</span><span class="p">.</span><span class="n" style="color: #333;">pop</span><span class="p">();</span></span>
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<pre style="margin: 0;">+<span id="LC36" 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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<pre style="margin: 0;">+<span id="LC37" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">lock_guard</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">mutex</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">lk</span><span class="p">(</span><span class="n" style="color: #333;">mut</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">data_queue</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="cpp"><span class="p">};</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="cpp"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">thread_pool</span></span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="cpp"><span class="p">{</span></span>
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47
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<pre style="margin: 0;">+<span id="LC47" 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;">atomic_bool</span> <span class="n" style="color: #333;">done</span><span class="p">;</span></span>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="cpp"> <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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49
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<pre style="margin: 0;">+<span id="LC49" 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;">map</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kr" style="font-weight: 600;">thread</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">id</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;">thread_id</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="cpp"> <span class="n" style="color: #333;">threadsafe_queue</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;">function</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">void</span><span class="p">()</span><span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">work_queue</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="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kr" style="font-weight: 600;">thread</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">threads</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC52" 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;">condition_variable</span> <span class="n" style="color: #333;">cv</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">mutex</span> <span class="n" style="color: #333;">m</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">worker_thread</span><span class="p">()</span> <span class="p">{</span></span>
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="cpp"> <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;">done</span><span class="p">)</span> <span class="p">{</span></span>
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">function</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">void</span><span class="p">()</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">task</span><span class="p">;</span></span>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">work_queue</span><span class="p">.</span><span class="n" style="color: #333;">try_pop</span><span class="p">(</span><span class="n" style="color: #333;">task</span><span class="p">))</span> <span class="p">{</span></span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="cpp"> <span class="n" style="color: #333;">task</span><span class="p">();</span></span>
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60
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<pre style="margin: 0;">+<span id="LC60" 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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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">unique_lock</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">mutex</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">lock</span><span class="p">(</span><span class="n" style="color: #333;">m</span><span class="p">);</span></span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="cpp"> <span class="n" style="color: #333;">cv</span><span class="p">.</span><span class="n" style="color: #333;">wait</span><span class="p">(</span><span class="n" style="color: #333;">lock</span><span class="p">,</span> <span class="p">[</span><span class="o" style="font-weight: 600;">&</span><span class="p">]</span> <span class="p">{</span><span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">work_queue</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">done</span><span class="p">;</span> <span class="p">});</span></span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="cpp"> <span class="p">}</span></span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="cpp"> <span class="p">}</span></span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="cpp"> <span class="p">}</span></span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="cpp"><span class="nl">public:</span></span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="cpp"> <span class="n" style="color: #333;">thread_pool</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nthr</span><span class="p">)</span><span class="o" style="font-weight: 600;">:</span></span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="cpp"> <span class="n" style="color: #333;">done</span><span class="p">(</span><span class="nb" style="color: #0086b3;">false</span><span class="p">),</span> <span class="n" style="color: #333;">nthreads</span><span class="p">(</span><span class="n" style="color: #333;">nthr</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="cpp"> <span class="p">{</span></span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">try</span> <span class="p">{</span></span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="cpp"> <span class="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;">nthreads</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="p">{</span></span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="cpp"> <span class="n" style="color: #333;">threads</span><span class="p">.</span><span class="n" style="color: #333;">emplace_back</span><span class="p">(</span></span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kr" style="font-weight: 600;">thread</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">thread_pool</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">worker_thread</span><span class="p">,</span> <span class="k" style="font-weight: 600;">this</span><span class="p">));</span></span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="cpp"> <span class="n" style="color: #333;">thread_id</span><span class="p">[</span><span class="n" style="color: #333;">threads</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">get_id</span><span class="p">()]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</span><span class="p">;</span></span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="cpp"> <span class="p">}</span></span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">catch</span> <span class="p">(...)</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;">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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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">throw</span><span class="p">;</span></span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="cpp"> <span class="p">}</span></span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="cpp"> <span class="p">}</span></span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">~</span><span class="n" style="color: #333;">thread_pool</span><span class="p">()</span> <span class="p">{</span></span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">nthreads</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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83
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<pre style="margin: 0;">+<span id="LC83" 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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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">unique_lock</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">mutex</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">lock</span><span class="p">(</span><span class="n" style="color: #333;">m</span><span class="p">);</span></span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="cpp"> <span class="n" style="color: #333;">cv</span><span class="p">.</span><span class="n" style="color: #333;">notify_all</span><span class="p">();</span></span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="cpp"> <span class="n" style="color: #333;">lock</span><span class="p">.</span><span class="n" style="color: #333;">unlock</span><span class="p">();</span></span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kr" style="font-weight: 600;">thread</span> <span class="o" style="font-weight: 600;">&</span><span class="kr" style="font-weight: 600;">thread</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">threads</span><span class="p">)</span> <span class="p">{</span></span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="cpp"> <span class="kr" style="font-weight: 600;">thread</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">();</span></span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="cpp"> <span class="p">}</span></span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="cpp"> <span class="p">}</span></span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="cpp"> <span class="p">}</span></span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="cpp"></span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">template</span><span class="o" style="font-weight: 600;"><</span><span class="k" style="font-weight: 600;">typename</span> <span class="nc" style="color: #458; font-weight: 600;">Function</span><span class="p">,</span> <span class="k" style="font-weight: 600;">typename</span><span class="o" style="font-weight: 600;">...</span> <span class="nc" style="color: #458; font-weight: 600;">Args</span><span class="p">></span></span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">future</span><span class="o" style="font-weight: 600;"><</span><span class="k" style="font-weight: 600;">typename</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">result_of</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Function</span><span class="p">(</span><span class="n" style="color: #333;">Args</span><span class="p">...)</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">type</span><span class="o" style="font-weight: 600;">></span></span>
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="cpp"> <span class="n" style="color: #333;">submit</span><span class="p">(</span><span class="n" style="color: #333;">Function</span> <span class="o" style="font-weight: 600;">&&</span><span class="n" style="color: #333;">f</span><span class="p">,</span> <span class="n" style="color: #333;">Args</span><span class="o" style="font-weight: 600;">&&</span><span class="p">...</span> <span class="n" style="color: #333;">args</span><span class="p">)</span> <span class="p">{</span></span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">using</span> <span class="n" style="color: #333;">result_type</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">typename</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">result_of</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Function</span><span class="p">(</span><span class="n" style="color: #333;">Args</span><span class="p">...)</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">type</span><span class="p">;</span></span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">auto</span> <span class="n" style="color: #333;">task</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;">make_shared</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;">packaged_task</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">result_type</span><span class="p">()</span><span class="o" style="font-weight: 600;">>></span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">bind</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">forward</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Function</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">),</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">forward</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Args</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">)...));</span></span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">future</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">result_type</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;">task</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">get_future</span><span class="p">());</span></span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="cpp"> <span class="n" style="color: #333;">work_queue</span><span class="p">.</span><span class="n" style="color: #333;">push</span><span class="p">([</span><span class="n" style="color: #333;">task</span><span class="p">]</span> <span class="p">{</span> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">task</span><span class="p">)();</span> <span class="p">});</span></span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">unique_lock</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">mutex</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">lock</span><span class="p">(</span><span class="n" style="color: #333;">m</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="cpp"> <span class="n" style="color: #333;">cv</span><span class="p">.</span><span class="n" style="color: #333;">notify_one</span><span class="p">();</span></span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">res</span><span class="p">;</span></span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="cpp"> <span class="p">}</span></span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="cpp"></span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="p">{</span></span>
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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;">return</span> <span class="n" style="color: #333;">nthreads</span><span class="p">;</span></span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="cpp"> <span class="p">}</span></span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="cpp"></span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">thread_id_to_int</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="kr" style="font-weight: 600;">thread</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">id</span> <span class="n" style="color: #333;">id</span><span class="p">)</span> <span class="p">{</span></span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">thread_id</span><span class="p">[</span><span class="n" style="color: #333;">id</span><span class="p">];</span></span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="cpp"> <span class="p">}</span></span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="cpp"></span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">template</span><span class="o" style="font-weight: 600;"><</span><span class="k" style="font-weight: 600;">typename</span> <span class="nc" style="color: #458; font-weight: 600;">T</span><span class="p">,</span> <span class="k" style="font-weight: 600;">typename</span> <span class="nc" style="color: #458; font-weight: 600;">Function</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="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">parallel_for</span><span class="p">(</span><span class="n" style="color: #333;">T</span> <span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="n" style="color: #333;">T</span> <span class="n" style="color: #333;">end</span><span class="p">,</span> <span class="n" style="color: #333;">T</span> <span class="n" style="color: #333;">stride</span><span class="p">,</span> <span class="n" style="color: #333;">Function</span> <span class="o" style="font-weight: 600;">&&</span><span class="n" style="color: #333;">f</span><span class="p">)</span> <span class="p">{</span></span>
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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="cpp"> <span class="n" style="color: #333;">T</span> <span class="n" style="color: #333;">range</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">start</span><span class="p">;</span></span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="cpp"> <span class="n" style="color: #333;">T</span> <span class="n" style="color: #333;">block_size</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">range</span> <span class="o" style="font-weight: 600;">/</span> <span class="p">(</span><span class="n" style="color: #333;">nthreads</span><span class="p">);</span></span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="cpp"> <span class="n" style="color: #333;">T</span> <span class="n" style="color: #333;">block_start</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">start</span><span class="p">;</span></span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="cpp"> <span class="n" style="color: #333;">T</span> <span class="n" style="color: #333;">block_end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">block_start</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">block_size</span><span class="p">;</span></span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">block_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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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="cpp"> <span class="n" style="color: #333;">block_end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">end</span><span class="p">;</span></span>
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">future</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">void</span><span class="o" style="font-weight: 600;">>></span> <span class="n" style="color: #333;">res</span><span class="p">;</span></span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">block_start</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">end</span><span class="p">)</span> <span class="p">{</span></span>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="cpp"> <span class="n" style="color: #333;">res</span><span class="p">.</span><span class="n" style="color: #333;">emplace_back</span><span class="p">(</span><span class="n" style="color: #333;">submit</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">,</span> <span class="n" style="color: #333;">block_start</span><span class="p">,</span> <span class="n" style="color: #333;">block_end</span><span class="p">,</span> <span class="n" style="color: #333;">stride</span><span class="p">));</span></span>
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124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="cpp"> <span class="n" style="color: #333;">block_start</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">block_end</span><span class="p">;</span></span>
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125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="cpp"> <span class="n" style="color: #333;">block_end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">block_end</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">block_size</span><span class="p">;</span></span>
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126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">block_end</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">end</span><span class="p">)</span></span>
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127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="cpp"> <span class="n" style="color: #333;">block_end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">end</span><span class="p">;</span></span>
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128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="cpp"> <span class="p">}</span></span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">res</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="cpp"> <span class="n" style="color: #333;">res</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">get</span><span class="p">();</span></span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="cpp"> <span class="p">}</span></span>
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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="cpp"><span class="p">};</span></span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="cpp"></span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span></pre>
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