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<h3>
Andreas Tille pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/bowtie">Debian Med / bowtie</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/bowtie/-/commit/f1445fa79fcadc47579571e81078e2231990074c">f1445fa7</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2021-09-14T06:48:20+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 1.3.1+dfsg</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bowtie/-/commit/9bf017434a90cf99f756c6ce9e222a7ed0c86a44">9bf01743</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2021-09-14T06:53:39+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 1.3.1</pre>
</li>
</ul>
<h4>23 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#cf83fa67117337dc6c425f166a2d9415dd59047a">
<span class="new-file">
+
.github/workflows/random_tests.yml
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</li>
<li class="file-stats">
<a href="#b62e40e78d290dda60201f0671b337deb7fc7491">
<span class="new-file">
+
.github/workflows/simple_tests.yml
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</li>
<li class="file-stats">
<a href="#dea01dd89a3b602828e630677fde5d77c06441c8">
.travis.yml
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<li class="file-stats">
<a href="#836efb6e25a091dcb4ff8e1dbb2f0be6a5cbf14c">
Makefile
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<li class="file-stats">
<a href="#9f621eb5fd3bcb2fa5c7bd228c9b1ad42edc46c8">
NEWS
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<li class="file-stats">
<a href="#b33892fbddeffc3368077b4904ad0b3d562a7312">
VERSION
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<li class="file-stats">
<a href="#dfe5e559b6d490c25075d3912c6d2202202c6f72">
bowtie-inspect
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<li class="file-stats">
<a href="#26bd7718783ad8eb99119709aba9650e1414efdb">
bt2_locks.cpp
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<li class="file-stats">
<a href="#ad2755e711011bd362f96ff15c058770229abd85">
bt2_locks.h
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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="#bdf1fda883543f04c4a046fdcaa8ba0db73fdb37">
ebwt.h
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<li class="file-stats">
<a href="#69652f4e3eff95542ec1637fffb5d028d18a5a54">
ebwt_search_util.h
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<li class="file-stats">
<a href="#9a66ef5c5fbb28475032abcc5eae532d03bd29f3">
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genomes/.cvsignore
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<li class="file-stats">
<a href="#f06297a2ada54367ed9d9c768f848c4726441af2">
hit.h
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<li class="file-stats">
<a href="#88d2b0f7968c3acf1acde0c4814002d780087895">
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+
mem_ids.h
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<li class="file-stats">
<a href="#d29fd14304274912c3f57246f6c1ac7e34eab154">
multikey_qsort.h
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<li class="file-stats">
<a href="#cc60758ea89135534b00a4c0ae3e29ee95c0ef25">
scripts/bowtie-hbb.sh
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<li class="file-stats">
<a href="#1ba32b1a76b5b57a56e4d834114b45c9fbeb218e">
shmem.h
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<li class="file-stats">
<a href="#660ce3632dfae6bcb8dd9430bc227c1af48265ec">
threading.h
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<li class="file-stats">
<a href="#26207b119752bd3d9fe20ed0efc42bec280de0eb">
tinythread.cpp
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<li class="file-stats">
<a href="#54b33722b92cc6ac990c217292b257c08318a6a5">
util.h
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</ul>
<h4>Changes:</h4>
<li id="cf83fa67117337dc6c425f166a2d9415dd59047a">
<a href="https://salsa.debian.org/med-team/bowtie/-/compare/fb3a91ce60d73bf653156f07370b7b34ba81ad97...9bf017434a90cf99f756c6ce9e222a7ed0c86a44#cf83fa67117337dc6c425f166a2d9415dd59047a"><strong>.github/workflows/random_tests.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;">Run bowtie random tests for all commits to master 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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<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;">master'</span></span>
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<pre style="margin: 0;">+<span id="LC6" 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="LC7" class="line" lang="yaml"> <span class="pi">-</span> <span class="s1" style="color: #d14;">'</span><span class="s" style="color: #d14;">**.c'</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;">bowtie'</span></span>
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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;">bowtie-build'</span></span>
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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;">bowtie-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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<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/test/**'</span></span>
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<pre style="margin: 0;">+<span id="LC15" 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="LC16" 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="LC17" 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="LC18" class="line" lang="yaml"> <span class="na" style="color: #008080;">paths</span><span class="pi">:</span></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="yaml"> <span class="pi">-</span> <span class="s1" style="color: #d14;">'</span><span class="s" style="color: #d14;">**.c'</span></span>
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20
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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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21
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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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22
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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;">bowtie'</span></span>
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23
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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;">bowtie-build'</span></span>
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24
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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;">bowtie-inspect'</span></span>
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25
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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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26
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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/test/**'</span></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="yaml"><span class="na" style="color: #008080;">jobs</span><span class="pi">:</span></span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="yaml"> <span class="na" style="color: #008080;">setup</span><span class="pi">:</span></span>
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29
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<pre style="margin: 0;">+<span id="LC29" 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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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="yaml"> <span class="na" style="color: #008080;">steps</span><span class="pi">:</span></span>
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31
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<pre style="margin: 0;">+<span id="LC31" 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;">Check out repository code</span></span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="yaml"> <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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33
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<pre style="margin: 0;">+<span id="LC33" 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;">Install zlib development files</span></span>
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34
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<pre style="margin: 0;">+<span id="LC34" 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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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="yaml"> <span class="s" style="color: #d14;">sudo apt-get update</span></span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="yaml"> <span class="s" style="color: #d14;">sudo apt-get install zlib1g-dev</span></span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="yaml"> <span class="na" style="color: #008080;">linux</span><span class="pi">:</span></span>
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38
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<pre style="margin: 0;">+<span id="LC38" 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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39
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<pre style="margin: 0;">+<span id="LC39" 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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40
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<pre style="margin: 0;">+<span id="LC40" 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="LC41" 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="LC42" 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 random tests</span></span>
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<pre style="margin: 0;">+<span id="LC43" 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="LC44" class="line" lang="yaml"> <span class="s" style="color: #d14;">make allall</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="yaml"> <span class="s" style="color: #d14;">make random-test</span></span>
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<pre style="margin: 0;">+<span id="LC46" 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="LC47" 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="LC48" 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="LC49" 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="LC50" 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 random tests</span></span>
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<pre style="margin: 0;">+<span id="LC51" 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="LC52" class="line" lang="yaml"> <span class="s" style="color: #d14;">make allall</span></span>
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<pre style="margin: 0;">+<span id="LC53" 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/bowtie/-/compare/fb3a91ce60d73bf653156f07370b7b34ba81ad97...9bf017434a90cf99f756c6ce9e222a7ed0c86a44#b62e40e78d290dda60201f0671b337deb7fc7491"><strong>.github/workflows/simple_tests.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;">Run bowtie simple tests 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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<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;">**.c'</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;">**.h'</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;">**.cpp'</span></span>
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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;">bowtie'</span></span>
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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;">bowtie-build'</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;">bowtie-inspect'</span></span>
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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;">Makefile'</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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16
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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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17
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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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18
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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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19
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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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20
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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;">**.c'</span></span>
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21
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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;">**.h'</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;">**.cpp'</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;">bowtie'</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;">bowtie-build'</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;">bowtie-inspect'</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;">Makefile'</span></span>
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27
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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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28
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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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29
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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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30
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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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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="yaml"> <span class="na" style="color: #008080;">steps</span><span class="pi">:</span></span>
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32
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<pre style="margin: 0;">+<span id="LC32" 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;">Check out repository code</span></span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="yaml"> <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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34
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<pre style="margin: 0;">+<span id="LC34" 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;">Install zlib development files</span></span>
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<pre style="margin: 0;">+<span id="LC35" 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="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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<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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<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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<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="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="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></pre>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="yaml"><span class="na" style="color: #008080;">dist</span><span class="pi">:</span> <span class="s" style="color: #d14;"><span class="idiff left right">xenial</span></span></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="yaml"><span class="na" style="color: #008080;">dist</span><span class="pi">:</span> <span class="s" style="color: #d14;"><span class="idiff left right">bionic</span></span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="yaml"><span class="na" style="color: #008080;">language</span><span class="pi">:</span> <span class="s" style="color: #d14;">cpp</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="yaml"><span class="na" style="color: #008080;">sudo</span><span class="pi">:</span> <span class="s" style="color: #d14;">required</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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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -7,45 +7,6 @@ branches:</td>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">bug_fixes</span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="yaml"><span class="na" style="color: #008080;">matrix</span><span class="pi">:</span></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="yaml"> <span class="na" style="color: #008080;">include</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="yaml"> <span class="c1" style="color: #998; font-style: italic;"># Linux (gcc4.9)</span></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">os</span><span class="pi">:</span> <span class="s" style="color: #d14;">linux</span></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="yaml"> <span class="na" style="color: #008080;">language</span><span class="pi">:</span> <span class="s" style="color: #d14;">python</span></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="yaml"> <span class="na" style="color: #008080;">python</span><span class="pi">:</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">3.4"</span></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="yaml"> <span class="na" style="color: #008080;">addons</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="yaml"> <span class="na" style="color: #008080;">apt</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="yaml"> <span class="na" style="color: #008080;">sources</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">ubuntu-toolchain-r-test</span></span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="yaml"> <span class="na" style="color: #008080;">packages</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">g++-4.9</span></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">zlib1g-dev</span></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="yaml"> <span class="na" style="color: #008080;">env</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">CC=gcc-4.9</span></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">CXX=g++-4.9</span></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="yaml"> <span class="c1" style="color: #998; font-style: italic;"># Linux (gcc8)</span></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">os</span><span class="pi">:</span> <span class="s" style="color: #d14;">linux</span></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="yaml"> <span class="na" style="color: #008080;">language</span><span class="pi">:</span> <span class="s" style="color: #d14;">python</span></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="yaml"> <span class="na" style="color: #008080;">python</span><span class="pi">:</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">3.8"</span></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="yaml"> <span class="na" style="color: #008080;">addons</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;">apt</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;">sources</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">ubuntu-toolchain-r-test</span></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="yaml"> <span class="na" style="color: #008080;">packages</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">g++-8</span></span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">zlib1g-dev</span></span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="yaml"> <span class="na" style="color: #008080;">env</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">CC=gcc-8</span></span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">CXX=g++-8</span></span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">CXXFLAGS="-fuse-ld=gold"</span></span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="yaml"> <span class="c1" style="color: #998; font-style: italic;"># MacOS</span></span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">os</span><span class="pi">:</span> <span class="s" style="color: #d14;">osx</span></span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="yaml"> <span class="na" style="color: #008080;">osx_image</span><span class="pi">:</span> <span class="s" style="color: #d14;">xcode11.2</span></span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="yaml"> <span class="na" style="color: #008080;">compiler</span><span class="pi">:</span> <span class="s" style="color: #d14;">clang</span></span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="yaml"> <span class="na" style="color: #008080;">env</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">CC=clang</span></span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">CXX=clang++</span></span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">NPROC="$(sysctl -n hw.activecpu)"</span></span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="yaml"> <span class="na" style="color: #008080;">before_install</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">brew unlink python@2</span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="yaml"> <span class="c1" style="color: #998; font-style: italic;"># ARM 64-bit</span></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">os</span><span class="pi">:</span> <span class="s" style="color: #d14;">linux</span></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="yaml"> <span class="na" style="color: #008080;">arch</span><span class="pi">:</span> <span class="s" style="color: #d14;">arm64</span></span>
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<a href="https://salsa.debian.org/med-team/bowtie/-/compare/fb3a91ce60d73bf653156f07370b7b34ba81ad97...9bf017434a90cf99f756c6ce9e222a7ed0c86a44#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">@@ -7,7 +7,7 @@ bindir = $(prefix)/bin</td>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="make"></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="make"><span class="nv" style="color: #008080;">ARCH</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">$(</span><span class="nb" style="color: #0086b3;">shell</span> <span class="nb" style="color: #0086b3;">uname</span> <span class="nt" style="color: #000080;">-m</span><span class="nf" style="color: #900; font-weight: 600;">)</span></span>
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9
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="make"><span class="nv" style="color: #008080;">INC</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">$(</span><span class="nb" style="color: #0086b3;">if</span> <span class="nv" style="color: #008080;">$(RELEASE_BUILD)</span>,-I<span class="nv" style="color: #008080;">$(CURDIR)</span>/.include<span class="nf" style="color: #900; font-weight: 600;">)</span> <span class="nt" style="color: #000080;">-I</span> third_party</span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="make"><span class="nv" style="color: #008080;">LIBS</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$(LDFLAGS)</span> <span class="nf" style="color: #900; font-weight: 600;">$(</span><span class="nb" style="color: #0086b3;">if</span> <span class="nv" style="color: #008080;">$(RELEASE_BUILD)</span>,-L<span class="nv" style="color: #008080;">$(CURDIR)</span>/.lib<span class="nf" style="color: #900; font-weight: 600;">)</span> <span class="nt" style="color: #000080;">-lz</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="make"><span class="nv" style="color: #008080;">LIBS</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$(LDFLAGS)</span> <span class="nf" style="color: #900; font-weight: 600;">$(</span><span class="nb" style="color: #0086b3;">if</span> <span class="nv" style="color: #008080;">$(RELEASE_BUILD)</span>,-L<span class="nv" style="color: #008080;">$(CURDIR)</span>/.lib<span class="nf" style="color: #900; font-weight: 600;">)</span> <span class="nt" style="color: #000080;">-lz</span><span class="idiff left"> </span><span class="nt" style="color: #000080;"><span class="idiff right">-lpthread</span></span></span>
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11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="make"><span class="nv" style="color: #008080;">HEADERS</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">$(</span><span class="nb" style="color: #0086b3;">wildcard</span> <span class="k" style="font-weight: 600;">*</span>.h<span class="nf" style="color: #900; font-weight: 600;">)</span></span>
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12
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="make"><span class="nv" style="color: #008080;">BOWTIE_MM</span> <span class="o" style="font-weight: 600;">=</span> 1</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="make"><span class="nv" style="color: #008080;">BOWTIE_SHARED_MEM</span> <span class="o" style="font-weight: 600;">=</span> 1</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="65" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -65,25 +65,9 @@ SHMEM_DEF =</td>
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="make"><span class="k" style="font-weight: 600;">ifeq</span> <span class="nv" style="color: #008080;">(1,$(BOWTIE_SHARED_MEM))</span></span>
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66
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="make"> <span class="nv" style="color: #008080;">SHMEM_DEF</span> <span class="o" style="font-weight: 600;">=</span> <span class="nt" style="color: #000080;">-DBOWTIE_SHARED_MEM</span></span>
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="make"><span class="k" style="font-weight: 600;">endif</span></span>
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<pre style="margin: 0;">-<span id="LC68" class="line" lang="make"><span class="nv" style="color: #008080;">PTHREAD_PKG</span> <span class="o" style="font-weight: 600;">=</span></span>
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69
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="make"><span class="nv" style="color: #008080;">PTHREAD_LIB</span> <span class="o" style="font-weight: 600;">=</span></span>
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="make"><span class="nv" style="color: #008080;">PTHREAD_DEF</span> <span class="o" style="font-weight: 600;">=</span></span>
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="make"></span>
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="make"><span class="k" style="font-weight: 600;">ifeq</span> <span class="nv" style="color: #008080;">(1,$(MINGW))</span></span>
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<pre style="margin: 0;">-<span id="LC73" class="line" lang="make"> <span class="nv" style="color: #008080;">PTHREAD_LIB</span> <span class="o" style="font-weight: 600;">=</span> </span>
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="make"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">override</span> <span class="nv" style="color: #008080;">EXTRA_FLAGS</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="LC75" class="line" lang="make"><span class="k" style="font-weight: 600;">else</span></span>
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<pre style="margin: 0;">-<span id="LC76" class="line" lang="make"> <span class="nv" style="color: #008080;">PTHREAD_LIB</span> <span class="o" style="font-weight: 600;">=</span> <span class="nt" style="color: #000080;">-lpthread</span></span>
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<pre style="margin: 0;">-<span id="LC77" class="line" lang="make"><span class="k" style="font-weight: 600;">endif</span></span>
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<pre style="margin: 0;">-<span id="LC78" class="line" lang="make"></span>
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<pre style="margin: 0;">-<span id="LC79" class="line" lang="make"><span class="k" style="font-weight: 600;">ifeq</span> <span class="nv" style="color: #008080;">(1,$(NO_SPINLOCK))</span></span>
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<pre style="margin: 0;">-<span id="LC80" class="line" lang="make"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">override</span> <span class="nv" style="color: #008080;">EXTRA_FLAGS</span> <span class="o" style="font-weight: 600;">+=</span> <span class="nt" style="color: #000080;">-DNO_SPINLOCK</span></span>
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<pre style="margin: 0;">-<span id="LC81" class="line" lang="make"><span class="k" style="font-weight: 600;">endif</span></span>
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<pre style="margin: 0;">-<span id="LC82" class="line" lang="make"></span>
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<pre style="margin: 0;">-<span id="LC83" class="line" lang="make"></span>
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<pre style="margin: 0;">-<span id="LC84" class="line" lang="make"><span class="nv" style="color: #008080;">LIBS</span> <span class="o" style="font-weight: 600;">+=</span> <span class="nv" style="color: #008080;">$(PTHREAD_LIB)</span></span>
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<pre style="margin: 0;">-<span id="LC85" class="line" lang="make"><span class="k" style="font-weight: 600;">ifeq</span> <span class="nv" style="color: #008080;">(1, $(WITH_TBBMALLOC))</span></span>
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<pre style="margin: 0;">-<span id="LC86" class="line" lang="make"> <span class="nv" style="color: #008080;">LIBS</span> <span class="o" style="font-weight: 600;">+=</span> <span class="nt" style="color: #000080;">-ltbbmalloc</span></span>
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="make"><span class="k" style="font-weight: 600;">endif</span></span>
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="make"></span>
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="make"><span class="nv" style="color: #008080;">POPCNT_CAPABILITY</span> <span class="o" style="font-weight: 600;">?=</span> 1</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="92" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="76" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -92,7 +76,6 @@ ifeq (aarch64,$(shell uname -m))</td>
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="make"><span class="k" style="font-weight: 600;">endif</span></span>
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="make"><span class="k" style="font-weight: 600;">ifeq</span> <span class="nv" style="color: #008080;">(1, $(POPCNT_CAPABILITY))</span></span>
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94
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78
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="make"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">override</span> <span class="nv" style="color: #008080;">EXTRA_FLAGS</span> <span class="o" style="font-weight: 600;">+=</span> <span class="nt" style="color: #000080;">-DPOPCNT_CAPABILITY</span></span>
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95
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<pre style="margin: 0;">-<span id="LC95" class="line" lang="make"> <span class="nv" style="color: #008080;">INC</span> <span class="o" style="font-weight: 600;">+=</span> <span class="nt" style="color: #000080;">-I</span> third_party</span>
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96
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79
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="make"><span class="k" style="font-weight: 600;">endif</span></span>
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97
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80
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="make"></span>
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98
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="make"><span class="nv" style="color: #008080;">PREFETCH_LOCALITY</span> <span class="o" style="font-weight: 600;">=</span> 2</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="113" style="width: 35px; color: rgba(0,0,0,0.3); 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="96" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -113,15 +96,16 @@ ifeq (1,$(WITH_THREAD_PROFILING))</td>
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113
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<pre style="margin: 0;"> <span id="LC96" class="line" lang="make"><span class="k" style="font-weight: 600;">endif</span></span>
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114
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97
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<pre style="margin: 0;"> <span id="LC97" class="line" lang="make"></span>
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115
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98
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<pre style="margin: 0;"> <span id="LC98" class="line" lang="make"><span class="nv" style="color: #008080;">OTHER_CPPS</span> <span class="o" style="font-weight: 600;">=</span> ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp <span class="se" style="color: #d14;">\</span></span>
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116
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<pre style="margin: 0;">-<span id="LC116" class="line" lang="make"> edit.cpp ebwt.cpp</span>
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="make"> edit.cpp ebwt.cpp<span class="idiff left right"> bt2_locks.cpp</span></span>
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="make"></span>
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<pre style="margin: 0;">-<span id="LC118" class="line" lang="make"><span class="k" style="font-weight: 600;">ifneq</span> <span class="nv" style="color: #008080;">(1, $(NO_SPINLOCK))</span></span>
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<pre style="margin: 0;">-<span id="LC119" class="line" lang="make"> <span class="nv" style="color: #008080;">OTHER_CPPS</span> <span class="o" style="font-weight: 600;">+=</span> bt2_locks.cpp</span>
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="make"><span class="k" style="font-weight: 600;">ifeq</span> <span class="nv" style="color: #008080;">(1,$(WITH_QUEUELOCK))</span></span>
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="make"> <span class="nv" style="color: #008080;">NO_SPINLOCK</span> <span class="o" style="font-weight: 600;">=</span> 1</span>
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="make"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">override</span> <span class="nv" style="color: #008080;">EXTRA_FLAGS</span> <span class="o" style="font-weight: 600;">+=</span> <span class="nt" style="color: #000080;">-DWITH_QUEUELOCK</span></span>
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<pre style="margin: 0;"> <span id="LC104" class="line" lang="make"><span class="k" style="font-weight: 600;">endif</span></span>
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<pre style="margin: 0;"> <span id="LC105" class="line" lang="make"></span>
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<pre style="margin: 0;">-<span id="LC122" class="line" lang="make"><span class="k" style="font-weight: 600;">ifeq</span> <span class="nv" style="color: #008080;">(1,$(<span class="idiff left right">WITH_QUEUE</span>LOCK))</span></span>
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123
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<pre style="margin: 0;">-<span id="LC123" class="line" lang="make"><span class="idiff left"> </span><span class="nv" style="color: #008080;"><span class="idiff">OTHER_CPPS</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+=</span></span><span class="idiff right"> bt2_locks.cpp</span></span>
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124
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<pre style="margin: 0;">-<span id="LC124" class="line" lang="make"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">override</span> <span class="nv" style="color: #008080;">EXTRA_FLAGS</span> <span class="o" style="font-weight: 600;">+=</span> <span class="nt" style="color: #000080;">-D<span class="idiff left">WITH_QUEUE</span>LOCK</span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff right">1</span></span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="make"><span class="k" style="font-weight: 600;">ifeq</span> <span class="nv" style="color: #008080;">(1,$(<span class="idiff left right">NO_SPIN</span>LOCK))</span></span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff left">$(info</span></span><span class="idiff"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff right">$(NO_SPINLOCK))</span></span></span>
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<td class="new_line diff-line-num new" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="make"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">override</span> <span class="nv" style="color: #008080;">EXTRA_FLAGS</span> <span class="o" style="font-weight: 600;">+=</span> <span class="nt" style="color: #000080;">-D<span class="idiff left right">NO_SPIN</span>LOCK</span></span>
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125
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109
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<pre style="margin: 0;"> <span id="LC109" class="line" lang="make"><span class="k" style="font-weight: 600;">endif</span></span>
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126
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110
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<pre style="margin: 0;"> <span id="LC110" class="line" lang="make"></span>
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127
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111
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<pre style="margin: 0;"> <span id="LC111" class="line" lang="make"><span class="k" style="font-weight: 600;">ifeq</span> <span class="nv" style="color: #008080;">(1,$(WITH_FINE_TIMER))</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="242" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="226" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -242,8 +226,8 @@ DEFS=-fno-strict-aliasing \</td>
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242
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226
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<pre style="margin: 0;"> <span id="LC226" class="line" lang="make"> <span class="nv" style="color: #008080;">$(SHMEM_DEF)</span></span>
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243
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227
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<pre style="margin: 0;"> <span id="LC227" class="line" lang="make"></span>
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244
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<pre style="margin: 0;"> <span id="LC228" class="line" lang="make"><span class="nv" style="color: #008080;">ALL_FLAGS</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$(EXTRA_FLAGS)</span> <span class="nv" style="color: #008080;">$(CFLAGS)</span> <span class="nv" style="color: #008080;">$(CXXFLAGS)</span></span>
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245
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<pre style="margin: 0;">-<span id="LC245" class="line" lang="make"><span class="nv" style="color: #008080;">DEBUG_DEFS</span> <span class="o" style="font-weight: 600;">=</span> <span class="nt" style="color: #000080;">-DCOMPILER_OPTIONS</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="se" style="color: #d14;">\"</span><span class="nv" style="color: #008080;">$(DEBUG_FLAGS)</span><span class="s2" style="color: #d14;"> </span><span class="nv" style="color: #008080;">$(<span class="idiff left right">ALL_</span>FLAGS)</span><span class="se" style="color: #d14;">\"</span><span class="s2" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">-<span id="LC246" class="line" lang="make"><span class="nv" style="color: #008080;">RELEASE_DEFS</span> <span class="o" style="font-weight: 600;">=</span> <span class="nt" style="color: #000080;">-DCOMPILER_OPTIONS</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="se" style="color: #d14;">\"</span><span class="nv" style="color: #008080;">$(RELEASE_FLAGS)</span><span class="s2" style="color: #d14;"> </span><span class="nv" style="color: #008080;">$(<span class="idiff left right">ALL_</span>FLAGS)</span><span class="se" style="color: #d14;">\"</span><span class="s2" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="make"><span class="nv" style="color: #008080;">DEBUG_DEFS</span> <span class="o" style="font-weight: 600;">=</span> <span class="nt" style="color: #000080;">-DCOMPILER_OPTIONS</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="se" style="color: #d14;">\"</span><span class="nv" style="color: #008080;">$(DEBUG_FLAGS)</span><span class="s2" style="color: #d14;"> </span><span class="nv" style="color: #008080;">$(<span class="idiff left">EXTRA_FLAGS)</span></span><span class="s2" style="color: #d14;"><span class="idiff"> </span></span><span class="nv" style="color: #008080;"><span class="idiff">$(CFLAGS)</span></span><span class="s2" style="color: #d14;"><span class="idiff"> </span></span><span class="nv" style="color: #008080;"><span class="idiff right">$(CXX</span>FLAGS)</span><span class="se" style="color: #d14;">\"</span><span class="s2" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">+<span id="LC230" class="line" lang="make"><span class="nv" style="color: #008080;">RELEASE_DEFS</span> <span class="o" style="font-weight: 600;">=</span> <span class="nt" style="color: #000080;">-DCOMPILER_OPTIONS</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="se" style="color: #d14;">\"</span><span class="nv" style="color: #008080;">$(RELEASE_FLAGS)</span><span class="s2" style="color: #d14;"> </span><span class="nv" style="color: #008080;">$(<span class="idiff left">EXTRA_FLAGS)</span></span><span class="s2" style="color: #d14;"><span class="idiff"> </span></span><span class="nv" style="color: #008080;"><span class="idiff">$(CFLAGS)</span></span><span class="s2" style="color: #d14;"><span class="idiff"> </span></span><span class="nv" style="color: #008080;"><span class="idiff right">$(CXX</span>FLAGS)</span><span class="se" style="color: #d14;">\"</span><span class="s2" style="color: #d14;">"</span></span>
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<pre style="margin: 0;"> <span id="LC231" class="line" lang="make"></span>
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232
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<pre style="margin: 0;"> <span id="LC232" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;">#</span></span>
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249
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233
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<pre style="margin: 0;"> <span id="LC233" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># bowtie-build targets</span></span>
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<li id="9f621eb5fd3bcb2fa5c7bd228c9b1ad42edc46c8">
<a href="https://salsa.debian.org/med-team/bowtie/-/compare/fb3a91ce60d73bf653156f07370b7b34ba81ad97...9bf017434a90cf99f756c6ce9e222a7ed0c86a44#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">@@ -5,7 +5,7 @@ Bowtie NEWS</td>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext"> Bowtie is now available for download. 0.9.0 is the first version to</span>
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7
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">be released under the OSI Artistic License (see `LICENSE') and freely</span>
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8
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext">available to the public for download. The current version is 1.3.<span class="idiff left right">0</span>.</span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">available to the public for download. The current version is 1.3.<span class="idiff left right">1</span>.</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"></span>
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10
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">Reporting Issues</span>
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11
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<pre style="margin: 0;"> <span id="LC11" 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">@@ -23,6 +23,18 @@ Keep up with our releases on the GitHub releases page:</td>
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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">Version Release History</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">Version 1.3.1 - Sep 13, 2021</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext"> * Fixed an overflow issue in `bowtie-build` that would sometimes</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext"> yield corrupt "large" (64-bit) indexes; the resulting index</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext"> would sometimes cause `bowtie` to hang. Note: `bowtie2-build`</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext"> does not have this issue.</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext"> * Fixed an issue in `bowtie` causing XM:i SAM optional field to</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext"> sometimes be off by 1 when using the `-m/-M` flags.</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext"> * Fixed an issue that would sometimes cause deadlocks in `bowtie`</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext"> when running multithreaded.</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext"> * Fixed an issue causing build errors when compiling against</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext"> a pre-C++11 standard.</span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="plaintext">Version 1.3.0 - Jul 22, 2020</span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="plaintext"></span>
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<a href="https://salsa.debian.org/med-team/bowtie/-/compare/fb3a91ce60d73bf653156f07370b7b34ba81ad97...9bf017434a90cf99f756c6ce9e222a7ed0c86a44#b33892fbddeffc3368077b4904ad0b3d562a7312"><strong>VERSION</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">1.3.<span class="idiff left right">0</span></span></pre>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">1.3.<span class="idiff left right">1</span></span></pre>
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<a href="https://salsa.debian.org/med-team/bowtie/-/compare/fb3a91ce60d73bf653156f07370b7b34ba81ad97...9bf017434a90cf99f756c6ce9e222a7ed0c86a44#dfe5e559b6d490c25075d3912c6d2202202c6f72"><strong>bowtie-inspect</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -21,7 +21,6 @@</td>
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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="LC23" 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="LC24" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">imp</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;">inspect</span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">importlib.machinery</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">SourceFileLoader</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;">logging</span></span>
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<a href="https://salsa.debian.org/med-team/bowtie/-/compare/fb3a91ce60d73bf653156f07370b7b34ba81ad97...9bf017434a90cf99f756c6ce9e222a7ed0c86a44#26bd7718783ad8eb99119709aba9650e1414efdb"><strong>bt2_locks.cpp</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "bt2_locks.h"</span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#if (__cplusplus >= 201103L)</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">mcs_lock</span><span class="o" style="font-weight: 600;">::</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="LC3" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "bt2_locks.h"</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">mcs_lock</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;">mcs_node</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">node</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="cpp"> <span class="n" style="color: #333;">node</span><span class="p">.</span><span class="n" style="color: #333;">next</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">nullptr</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="cpp"> <span class="n" style="color: #333;">node</span><span class="p">.</span><span class="n" style="color: #333;">unlocked</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="LC7" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="cpp"> <span class="n" style="color: #333;">mcs_node</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">pred</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">q</span><span class="p">.</span><span class="n" style="color: #333;">exchange</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">node</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;">memory_order_<span class="idiff left right">release</span></span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="cpp"> <span class="n" style="color: #333;">mcs_node</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">pred</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">q</span><span class="p">.</span><span class="n" style="color: #333;">exchange</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">node</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;">memory_order_<span class="idiff left right">acq_rel</span></span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">pred</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="cpp"> <span class="n" style="color: #333;">pred</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">next</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">node</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="cpp"> <span class="n" style="color: #333;">node</span><span class="p">.</span><span class="n" style="color: #333;">unlocked</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="LC11" class="line" lang="cpp"> <span class="n" style="color: #333;">pred</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">next</span><span class="p">.</span><span class="n" style="color: #333;">store</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">node</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;">memory_order_release</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="cpp"> <span class="n" style="color: #333;">spin_while_eq</span><span class="p">(</span><span class="n" style="color: #333;">node</span><span class="p">.</span><span class="n" style="color: #333;">unlocked</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="cpp"> <span class="n" style="color: #333;">node</span><span class="p">.</span><span class="n" style="color: #333;">unlocked</span><span class="p">.</span><span class="n" style="color: #333;">load</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;">memory_order_acquire</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">mcs_lock</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">unlock</span><span class="p">()</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC18" 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;">node</span><span class="p">.</span><span class="n" style="color: #333;">next</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">mcs_lock</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">unlock</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">mcs_node</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 right">node</span></span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC18" 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;">node</span><span class="p">.</span><span class="n" style="color: #333;">next</span><span class="p"><span class="idiff left">.</span></span><span class="n" style="color: #333;"><span class="idiff">load</span></span><span class="p"><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">memory_order_acquire</span></span><span class="p"><span class="idiff right">)</span>)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="cpp"> <span class="n" style="color: #333;">mcs_node</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">node_ptr</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">node</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="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">q</span><span class="p">.</span><span class="n" style="color: #333;">compare_exchange_strong</span><span class="p">(</span><span class="n" style="color: #333;">node_ptr</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="cpp"> <span class="p">(</span><span class="n" style="color: #333;">mcs_node</span> <span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="nb" style="color: #0086b3;">nullptr</span><span class="p">,</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); 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="23" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -23,10 +23,9 @@ void mcs_lock::unlock() {</td>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="cpp"> <span class="n" style="color: #333;">spin_while_eq</span><span class="p">(</span><span class="n" style="color: #333;">node</span><span class="p">.</span><span class="n" style="color: #333;">next</span><span class="p">,</span> <span class="p">(</span><span class="n" style="color: #333;">mcs_node</span> <span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="nb" style="color: #0086b3;">nullptr</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="cpp"> <span class="n" style="color: #333;">node</span><span class="p">.</span><span class="n" style="color: #333;">next</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">unlocked</span><span class="p">.</span><span class="n" style="color: #333;">store</span><span class="p">(</span><span class="nb" style="color: #0086b3;">true</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;">memory_order_release</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="cpp"> <span class="n" style="color: #333;">node</span><span class="p">.</span><span class="n" style="color: #333;">next</span><span class="p"><span class="idiff left">.</span></span><span class="n" style="color: #333;"><span class="idiff">load</span></span><span class="p"><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">memory_order_acquire</span></span><span class="p"><span class="idiff right">)</span></span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">unlocked</span><span class="p">.</span><span class="n" style="color: #333;">store</span><span class="p">(</span><span class="nb" style="color: #0086b3;">true</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;">memory_order_release</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="cpp"><span class="k" style="font-weight: 600;">thread_local</span> <span class="n" style="color: #333;">mcs_lock</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">mcs_node</span> <span class="n" style="color: #333;">mcs_lock</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">node</span><span class="p">;</span></span>
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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;">void</span> <span class="n" style="color: #333;">spin_lock</span><span class="o" style="font-weight: 600;">::</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="LC31" class="line" lang="cpp"> <span class="n" style="color: #333;">cpu_backoff</span> <span class="n" style="color: #333;">backoff</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); 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="36" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -37,4 +36,5 @@ void spin_lock::lock() {</td>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">spin_lock</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">unlock</span><span class="p">()</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="cpp"> <span class="n" style="color: #333;">flag</span><span class="p">.</span><span class="n" style="color: #333;">clear</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;">memory_order_release</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="cpp"></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;">#endif</span></span></pre>
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<a href="https://salsa.debian.org/med-team/bowtie/-/compare/fb3a91ce60d73bf653156f07370b7b34ba81ad97...9bf017434a90cf99f756c6ce9e222a7ed0c86a44#ad2755e711011bd362f96ff15c058770229abd85"><strong>bt2_locks.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">@@ -12,13 +12,17 @@</td>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="cpp"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">cpu_backoff</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="cpp"><span class="nl">public:</span></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="cpp"> <span class="n" style="color: #333;">cpu_backoff</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="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="LC15" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">pause</span><span class="p">()</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="cpp"> <span class="kr" style="font-weight: 600;"><span class="idiff left">inline</span></span><span class="idiff right"> </span><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">pause</span><span class="p">()</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">count</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">LOOPS_BEFORE_YIELD</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC17" 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;">int32_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;">count</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="LC18" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#ifdef __aarch64__</span></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="cpp"> <span class="n" style="color: #333;">__asm__</span> <span class="n" style="color: #333;">__volatile__</span><span class="p">(</span><span class="s" style="color: #d14;">"yield"</span> <span class="o" style="font-weight: 600;">:::</span> <span class="s" style="color: #d14;">"memory"</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#else</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#elif __ppc__</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="cpp"> <span class="n" style="color: #333;">__asm__</span> <span class="n" style="color: #333;">__volatile__</span><span class="p">(</span><span class="s" style="color: #d14;">"or 27,27,27"</span> <span class="o" style="font-weight: 600;">:::</span> <span class="s" style="color: #d14;">"memory"</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#elif __x86_64__</span></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="cpp"> <span class="n" style="color: #333;">__asm__</span> <span class="n" style="color: #333;">__volatile__</span><span class="p">(</span><span class="s" style="color: #d14;">"pause;"</span><span class="p">);</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;">#else</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// do nothing</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;">#endif</span></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="cpp"> <span class="n" style="color: #333;">count</span> <span class="o" style="font-weight: 600;">*=</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -44,27 +48,27 @@ class mcs_lock {</td>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="cpp"><span class="nl">public:</span></span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="cpp"> <span class="n" style="color: #333;">mcs_lock</span><span class="p">()</span><span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">q</span><span class="p">(</span><span class="nb" style="color: #0086b3;">nullptr</span><span class="p">)</span> <span class="p">{}</span></span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">mcs_node</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;">mcs_node</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">next</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC51" 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">atomic</span></span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="n" style="color: #333;">mcs_node</span> <span class="o" style="font-weight: 600;">*<span class="idiff">></span></span><span class="idiff right"> </span><span class="n" style="color: #333;">next</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;">atomic_bool</span> <span class="n" style="color: #333;">unlocked</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="cpp"> <span class="p">};</span></span>
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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="LC51" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">lock</span><span class="p">();</span></span>
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">unlock</span><span class="p">();</span></span>
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">typedef</span> <span class="n" style="color: #333;">mcs_node</span><span class="o" style="font-weight: 600;"><span class="idiff left right">*</span></span> <span class="n" style="color: #333;">mcs_node_ptr</span><span class="p">;</span></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;">lock</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">mcs_node</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 right">node</span></span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">unlock</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">mcs_node</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 right">node</span></span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">typedef</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">atomic</span></span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="n" style="color: #333;">mcs_node</span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff right">*></span></span> <span class="n" style="color: #333;">mcs_node_ptr</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="cpp"><span class="nl">private:</span></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;">spin_while_eq</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="k" style="font-weight: 600;">volatile</span> <span class="n" style="color: #333;">mcs_node_ptr</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">value</span><span class="p">,</span> <span class="n" style="color: #333;">mcs_node</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">expected</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">spin_while_eq</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="k" style="font-weight: 600;">volatile</span> <span class="n" style="color: #333;">mcs_node_ptr</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">value</span><span class="p">,</span> <span class="k" style="font-weight: 600;"><span class="idiff left">const</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">volatile</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">mcs_node</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">expected</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="cpp"> <span class="n" style="color: #333;">cpu_backoff</span> <span class="n" style="color: #333;">backoff</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">value</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">expected</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">value</span><span class="p"><span class="idiff left">.</span></span><span class="n" style="color: #333;"><span class="idiff">load</span></span><span class="p"><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">memory_order_acquire</span></span><span class="p"><span class="idiff right">)</span></span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">expected</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="cpp"> <span class="n" style="color: #333;">backoff</span><span class="p">.</span><span class="n" style="color: #333;">pause</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>
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">spin_while_eq</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="k" style="font-weight: 600;">volatile</span> <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="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">value</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">expected</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="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">spin_while_eq</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="k" style="font-weight: 600;">volatile</span> <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="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">value</span><span class="p">,</span> <span class="k" style="font-weight: 600;"><span class="idiff left">const</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">volatile</span></span><span class="idiff right"> </span><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">expected</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="cpp"> <span class="n" style="color: #333;">cpu_backoff</span> <span class="n" style="color: #333;">backoff</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">value</span><span class="p">.</span><span class="n" style="color: #333;">load</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;">memory_order_acquire</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">expected</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="cpp"> <span class="n" style="color: #333;">backoff</span><span class="p">.</span><span class="n" style="color: #333;">pause</span><span class="p">();</span></span>
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC70" 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</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">mcs_node</span> <span class="o" style="font-weight: 600;">*></span> <span class="n" style="color: #333;">q</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">thread_local</span> <span class="n" style="color: #333;">mcs_node</span> <span class="n" style="color: #333;">node</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="cpp"><span class="p">};</span></span>
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<pre style="margin: 0;">-<span id="LC69" 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="LC72" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#endif // if (__cplusplus >= 201103L)</span></span>
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#endif // __MCS_LOCK_H__</span></span></pre>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext"><h1>Table of Contents</h1></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext"><p>Bowtie 1.3.<span class="idiff left right">0</span></p></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"><p>Bowtie 1.3.<span class="idiff left right">1</span></p></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"><nav id="TOC" role="doc-toc"></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext"><h2>1.3.1 - 09/13/2021</h2></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> <li>Fixed an overflow issue in <code>bowtie-build</code> that would sometimes yield corrupt "large" (64-bit) indexes; the resulting index would sometimes cause <code>bowtie</code> to hang. Note: <code>bowtie2-build</code> does not have this issue.</li></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> <li>Fixed an issue in <code>bowtie</code> causing XM:i SAM optional field to sometimes be off by 1 when using the <code><a href="manual.shtml#bowtie-options-m">-m</a>/<a href="manual.shtml#bowtie-options-M">-M</a></code> flags.</li></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> <li>Fixed an issue that would sometimes cause deadlocks in <code>bowtie</code> when running multithreaded.</li></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> <li>Fixed an issue causing build errors when compiling against a pre-C++11 standard.</li></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"></ul></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"><h2>1.3.0 - 07/22/2020</h2></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"><ul></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> <li>Fixed an issue causing <code>bowtie</code> to report incorrect results when using a Bowtie 2 index.</li></span>
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<a href="https://salsa.debian.org/med-team/bowtie/-/compare/fb3a91ce60d73bf653156f07370b7b34ba81ad97...9bf017434a90cf99f756c6ce9e222a7ed0c86a44#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/bowtie/1.3.<span class="idiff left">0</span>">Bowtie 1.3.<span class="idiff right">0</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/bowtie/1.3.<span class="idiff left">1</span>">Bowtie 1.3.<span class="idiff right">1</span></a></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="plaintext"> 0<span class="idiff left">7/22</span>/2<span class="idiff right">0</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"> 0<span class="idiff left">9/13</span>/2<span class="idiff right">1</span></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext"> <tr></span>
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<a href="https://salsa.debian.org/med-team/bowtie/-/compare/fb3a91ce60d73bf653156f07370b7b34ba81ad97...9bf017434a90cf99f756c6ce9e222a7ed0c86a44#bdf1fda883543f04c4a046fdcaa8ba0db73fdb37"><strong>ebwt.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">@@ -36,6 +36,7 @@</td>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "threading.h"</span></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "timer.h"</span></span>
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<pre style="margin: 0;"> <span id="LC38" 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="LC39" 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;">#ifdef POPCNT_CAPABILITY</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 "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">@@ -206,7 +207,7 @@ public:</td>
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<pre style="margin: 0;"> <span id="LC207" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">sideSz</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;">_sideSz</span><span class="p">;</span> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC208" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">sideBwtSz</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;">_sideBwtSz</span><span class="p">;</span> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC209" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">sideBwtLen</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;">_sideBwtLen</span><span class="p">;</span> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC209" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right">uint32_t</span></span> <span class="n" style="color: #333;">numSidePairs</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;">_numSidePairs</span><span class="p">;</span> <span class="p">}</span> <span class="cm" style="color: #998; font-style: italic;">/* check */</span></span>
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left right">TIndexOffU</span></span> <span class="n" style="color: #333;">numSidePairs</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;">_numSidePairs</span><span class="p">;</span> <span class="p">}</span> <span class="cm" style="color: #998; font-style: italic;">/* check */</span></span>
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<pre style="margin: 0;"> <span id="LC211" class="line" lang="cpp"> <span class="n" style="color: #333;">TIndexOffU</span> <span class="n" style="color: #333;">numSides</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;">_numSides</span><span class="p">;</span> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC212" class="line" lang="cpp"> <span class="n" style="color: #333;">TIndexOffU</span> <span class="n" style="color: #333;">numLines</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;">_numLines</span><span class="p">;</span> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC213" class="line" lang="cpp"> <span class="n" style="color: #333;">TIndexOffU</span> <span class="n" style="color: #333;">ebwtTotLen</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;">_ebwtTotLen</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">@@ -310,7 +311,7 @@ public:</td>
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<pre style="margin: 0;"> <span id="LC311" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">_sideSz</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC312" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">_sideBwtSz</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC313" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">_sideBwtLen</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC313" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right">uint32_t</span></span> <span class="n" style="color: #333;">_numSidePairs</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC314" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left right">TIndexOffU</span></span> <span class="n" style="color: #333;">_numSidePairs</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC315" class="line" lang="cpp"> <span class="n" style="color: #333;">TIndexOffU</span> <span class="n" style="color: #333;">_numSides</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC316" class="line" lang="cpp"> <span class="n" style="color: #333;">TIndexOffU</span> <span class="n" style="color: #333;">_numLines</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC317" class="line" lang="cpp"> <span class="n" style="color: #333;">TIndexOffU</span> <span class="n" style="color: #333;">_ebwtTotLen</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">@@ -754,17 +755,17 @@ public:</td>
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755
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<pre style="margin: 0;"> <span id="LC755" class="line" lang="cpp"> <span class="n" style="color: #333;">dcv</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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756
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<pre style="margin: 0;"> <span id="LC756" class="line" lang="cpp"> <span class="n" style="color: #333;">TIndexOffU</span> <span class="n" style="color: #333;">sz</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;">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;">simulateAllocs</span><span class="p">(</span><span class="n" style="color: #333;">s</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;">1</span><span class="p">);</span></span>
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756
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757
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<pre style="margin: 0;"> <span id="LC757" 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;">1</span><span class="p">)</span> <span class="n" style="color: #333;">sz</span> <span class="o" style="font-weight: 600;">*=</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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<pre style="margin: 0;">-<span id="LC757" class="line" lang="cpp"> <span class="n" style="color: #333;">AutoArray</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;">tmp</span><span class="p">(</span><span class="n" style="color: #333;">sz</span><span class="p">);</span></span>
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758
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<pre style="margin: 0;">+<span id="LC758" class="line" lang="cpp"> <span class="n" style="color: #333;">AutoArray</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;">tmp</span><span class="p">(</span><span class="n" style="color: #333;">sz</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">EBWT_CAT</span></span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC759" class="line" lang="cpp"> <span class="n" style="color: #333;">dcv</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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760
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<pre style="margin: 0;"> <span id="LC760" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Likewise with the KarkkainenBlockwiseSA</span></span>
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761
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<pre style="margin: 0;"> <span id="LC761" class="line" lang="cpp"> <span class="n" style="color: #333;">sz</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;">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;">simulateAllocs</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>
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761
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<pre style="margin: 0;">-<span id="LC761" class="line" lang="cpp"> <span class="n" style="color: #333;">AutoArray</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;">tmp2</span><span class="p">(</span><span class="n" style="color: #333;">sz</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC762" class="line" lang="cpp"> <span class="n" style="color: #333;">AutoArray</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;">tmp2</span><span class="p">(</span><span class="n" style="color: #333;">sz</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">EBWT_CAT</span></span><span class="p">);</span></span>
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763
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<pre style="margin: 0;"> <span id="LC763" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Now throw in the 'ftab' and 'isaSample' structures</span></span>
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764
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<pre style="margin: 0;"> <span id="LC764" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// that we'll eventually allocate in buildToDisk</span></span>
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<pre style="margin: 0;">-<span id="LC764" class="line" lang="cpp"> <span class="n" style="color: #333;">AutoArray</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;">ftab</span><span class="p">(</span><span class="n" style="color: #333;">_eh</span><span class="p">.</span><span class="n" style="color: #333;">_ftabLen</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="LC765" class="line" lang="cpp"> <span class="n" style="color: #333;">AutoArray</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;">ftab</span><span class="p">(</span><span class="n" style="color: #333;">_eh</span><span class="p">.</span><span class="n" style="color: #333;">_ftabLen</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">2</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">EBWT_CAT</span></span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC766" class="line" lang="cpp"> <span class="n" style="color: #333;">AutoArray</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;">side</span><span class="p">(</span><span class="n" style="color: #333;">_eh</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="LC767" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Grab another 20 MB out of caution</span></span>
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<pre style="margin: 0;">-<span id="LC767" class="line" lang="cpp"> <span class="n" style="color: #333;">AutoArray</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;">extra</span><span class="p">(</span><span class="mi" style="color: #099;">20</span><span class="o" style="font-weight: 600;">*</span><span class="mi" style="color: #099;">1024</span><span class="o" style="font-weight: 600;">*</span><span class="mi" style="color: #099;">1024</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC768" class="line" lang="cpp"> <span class="n" style="color: #333;">AutoArray</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;">extra</span><span class="p">(</span><span class="mi" style="color: #099;">20</span><span class="o" style="font-weight: 600;">*</span><span class="mi" style="color: #099;">1024</span><span class="o" style="font-weight: 600;">*</span><span class="mi" style="color: #099;">1024</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">EBWT_CAT</span></span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC769" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// If we made it here without throwing bad_alloc, then we</span></span>
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<pre style="margin: 0;"> <span id="LC770" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// passed the memory-usage stress test</span></span>
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<pre style="margin: 0;"> <span id="LC771" class="line" lang="cpp"> <span class="n" style="color: #333;">VMSG</span><span class="p">(</span><span class="s" style="color: #d14;">" Passed! Constructing with these parameters: --bmax "</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="s" style="color: #d14;">" --dcv "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">dcv</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">@@ -3996,13 +3997,14 @@ void Ebwt::buildToDisk(InorderBlockwiseSA<TStr>& sa,</td>
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3996
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3997
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<pre style="margin: 0;"> <span id="LC3997" class="line" lang="cpp"> <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">sa</span><span class="p">.</span><span class="n" style="color: #333;">suffixItrIsReset</span><span class="p">());</span></span>
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3997
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3998
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<pre style="margin: 0;"> <span id="LC3998" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// assert_leq((int)ValueSize<Dna>::VALUE, 4);</span></span>
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3999
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<pre style="margin: 0;"> <span id="LC3999" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC3999" class="line" lang="cpp"> <span class="n" style="color: #333;">TIndexOffU</span> <span class="n" style="color: #333;">len</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;">_len</span><span class="p">;</span></span>
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4000
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<pre style="margin: 0;">-<span id="LC4000" class="line" lang="cpp"> <span class="n" style="color: #333;">TIndexOffU</span> <span class="n" style="color: #333;">ftabLen</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;">_ftabLen</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC4001" class="line" lang="cpp"> <span class="n" style="color: #333;">TIndexOffU</span> <span class="n" style="color: #333;">sideSz</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;">_sideSz</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC4002" class="line" lang="cpp"> <span class="n" style="color: #333;">TIndexOffU</span> <span class="n" style="color: #333;">ebwtTotSz</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;">_ebwtTotSz</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC4003" class="line" lang="cpp"> <span class="n" style="color: #333;">TIndexOffU</span> <span class="n" style="color: #333;">fchr</span><span class="p">[]</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="mi" style="color: #099;">0</span><span class="p">};</span></span>
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<pre style="margin: 0;">-<span id="LC4004" 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;">ftab</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="LC4005" class="line" lang="cpp"> <span class="n" style="color: #333;">TIndexOffU</span> <span class="n" style="color: #333;">zOff</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">OFF_MASK</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC4000" class="line" lang="cpp"> <span class="n" style="color: #333;">TIndexOffU</span> <span class="n" style="color: #333;">len</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;">_len</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC4001" class="line" lang="cpp"> <span class="n" style="color: #333;">TIndexOffU</span> <span class="n" style="color: #333;">ftabLen</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;">_ftabLen</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC4002" class="line" lang="cpp"> <span class="n" style="color: #333;">TIndexOffU</span> <span class="n" style="color: #333;">sideSz</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;">_sideSz</span><span class="p">;</span></span>
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4003
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<pre style="margin: 0;">+<span id="LC4003" class="line" lang="cpp"> <span class="n" style="color: #333;">TIndexOffU</span> <span class="n" style="color: #333;">ebwtTotSz</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;">_ebwtTotSz</span><span class="p">;</span></span>
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4004
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<pre style="margin: 0;">+<span id="LC4004" class="line" lang="cpp"> <span class="n" style="color: #333;">TIndexOffU</span> <span class="n" style="color: #333;">fchr</span><span class="p">[]</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="mi" style="color: #099;">0</span><span class="p">};</span></span>
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4005
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<pre style="margin: 0;">+<span id="LC4005" 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;">ftab</span><span class="p">(</span><span class="n" style="color: #333;">EBWT_CAT</span><span class="p">);</span></span>
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4006
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<pre style="margin: 0;">+<span id="LC4006" class="line" lang="cpp"> <span class="n" style="color: #333;">TIndexOffU</span> <span class="n" style="color: #333;">zOff</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">OFF_MASK</span><span class="p">;</span></span>
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4007
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<pre style="margin: 0;">+<span id="LC4007" class="line" lang="cpp"></span>
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4008
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<pre style="margin: 0;"> <span id="LC4008" class="line" lang="cpp"></span>
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4009
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<pre style="margin: 0;"> <span id="LC4009" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Save # of occurrences of each character as we walk along the bwt</span></span>
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4010
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<pre style="margin: 0;"> <span id="LC4010" class="line" lang="cpp"> <span class="n" style="color: #333;">TIndexOffU</span> <span class="n" style="color: #333;">occ</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">};</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -4013,42 +4015,42 @@ void Ebwt::buildToDisk(InorderBlockwiseSA<TStr>& sa,</td>
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4013
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4015
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<pre style="margin: 0;"> <span id="LC4015" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// The absorbed rows represent suffixes shorter than the ftabChars</span></span>
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4014
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4016
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<pre style="margin: 0;"> <span id="LC4016" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// cutoff.</span></span>
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4017
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<pre style="margin: 0;"> <span id="LC4017" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint8_t</span> <span class="n" style="color: #333;">absorbCnt</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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4016
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<pre style="margin: 0;">-<span id="LC4016" 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;">absorbFtab</span><span class="p">;</span></span>
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4018
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<pre style="margin: 0;">+<span id="LC4018" class="line" lang="cpp"> <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;">uint8_t</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">absorbFtab</span><span class="p">(</span><span class="n" style="color: #333;">EBWT_CAT</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC4019" class="line" lang="cpp"></span>
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4020
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<pre style="margin: 0;"> <span id="LC4020" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">try</span> <span class="p">{</span></span>
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4021
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<pre style="margin: 0;"> <span id="LC4021" class="line" lang="cpp"> <span class="n" style="color: #333;">VMSG_NL</span><span class="p">(</span><span class="s" style="color: #d14;">"Allocating ftab, absorbFtab"</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC4019" class="line" lang="cpp"> <span class="n" style="color: #333;">ftab</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">TIndexOffU</span><span class="p">[</span><span class="n" style="color: #333;">ftabLen</span><span class="p">];</span></span>
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4020
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<pre style="margin: 0;">-<span id="LC4020" class="line" lang="cpp"> <span class="n" style="color: #333;">memset</span><span class="p">(</span><span class="n" style="color: #333;">ftab</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">OFF_SIZE</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">ftabLen</span><span class="p">);</span></span>
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4021
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<pre style="margin: 0;">-<span id="LC4021" class="line" lang="cpp"> <span class="n" style="color: #333;">absorbFtab</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;">ftabLen</span><span class="p">];</span></span>
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<pre style="margin: 0;">-<span id="LC4022" class="line" lang="cpp"> <span class="n" style="color: #333;">memset</span><span class="p">(</span><span class="n" style="color: #333;">absorbFtab</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">ftabLen</span><span class="p">);</span></span>
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4022
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<pre style="margin: 0;">+<span id="LC4022" class="line" lang="cpp"> <span class="n" style="color: #333;">ftab</span><span class="p">.</span><span class="n" style="color: #333;">resize</span><span class="p">(</span><span class="n" style="color: #333;">ftabLen</span><span class="p">);</span></span>
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4023
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<pre style="margin: 0;">+<span id="LC4023" class="line" lang="cpp"> <span class="n" style="color: #333;">ftab</span><span class="p">.</span><span class="n" style="color: #333;">fillZero</span><span class="p">();</span></span>
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4024
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<pre style="margin: 0;">+<span id="LC4024" class="line" lang="cpp"> <span class="n" style="color: #333;">absorbFtab</span><span class="p">.</span><span class="n" style="color: #333;">resize</span><span class="p">(</span><span class="n" style="color: #333;">ftabLen</span><span class="p">);</span></span>
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4025
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<pre style="margin: 0;">+<span id="LC4025" class="line" lang="cpp"> <span class="n" style="color: #333;">absorbFtab</span><span class="p">.</span><span class="n" style="color: #333;">fillZero</span><span class="p">();</span></span>
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4026
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<pre style="margin: 0;">+<span id="LC4026" class="line" lang="cpp"></span>
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4027
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<pre style="margin: 0;"> <span id="LC4027" 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;">bad_alloc</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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4024
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4028
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<pre style="margin: 0;"> <span id="LC4028" 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;">"Out of memory allocating ftab[] or absorbFtab[] "</span></span>
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4025
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4029
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<pre style="margin: 0;"> <span id="LC4029" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"in Ebwt::buildToDisk() at "</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;">":"</span></span>
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4026
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4030
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<pre style="margin: 0;"> <span id="LC4030" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">__LINE__</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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4027
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4031
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<pre style="margin: 0;"> <span id="LC4031" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">throw</span> <span class="n" style="color: #333;">e</span><span class="p">;</span></span>
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4028
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4032
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<pre style="margin: 0;"> <span id="LC4032" class="line" lang="cpp"> <span class="p">}</span></span>
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4029
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<pre style="margin: 0;">-<span id="LC4029" class="line" lang="cpp"> <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">ftab</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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4030
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<pre style="margin: 0;">-<span id="LC4030" class="line" lang="cpp"> <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">absorbFtab</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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4033
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<pre style="margin: 0;"> <span id="LC4033" class="line" lang="cpp"></span>
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4032
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4034
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<pre style="margin: 0;"> <span id="LC4034" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Allocate the side buffer; holds a single side as its being</span></span>
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4033
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4035
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<pre style="margin: 0;"> <span id="LC4035" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// constructed and then written to disk. Reused across all sides.</span></span>
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4034
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4036
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<pre style="margin: 0;"> <span id="LC4036" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#ifdef SIXTY4_FORMAT</span></span>
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4035
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<pre style="margin: 0;">-<span id="LC4035" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="o" style="font-weight: 600;"><span class="idiff left">*</span></span><span class="n" style="color: #333;">ebwtSide</span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff right">NULL</span></span><span class="p">;</span></span>
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4037
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<pre style="margin: 0;">+<span id="LC4037" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">EList</span></span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="kt" style="color: #458; font-weight: 600;">uint64_t</span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span> <span class="n" style="color: #333;">ebwtSide</span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">EBWT_CAT</span></span><span class="p"><span class="idiff right">)</span>;</span></span>
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4036
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4038
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<pre style="margin: 0;"> <span id="LC4038" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#else</span></span>
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4037
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<pre style="margin: 0;">-<span id="LC4037" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint8_t</span> <span class="o" style="font-weight: 600;"><span class="idiff left">*</span></span><span class="n" style="color: #333;">ebwtSide</span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff right">NULL</span></span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC4039" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">EList</span></span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="kt" style="color: #458; font-weight: 600;">uint8_t</span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span> <span class="n" style="color: #333;">ebwtSide</span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">EBWT_CAT</span></span><span class="p"><span class="idiff right">)</span>;</span></span>
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4040
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<pre style="margin: 0;"> <span id="LC4040" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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4041
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<pre style="margin: 0;"> <span id="LC4041" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">try</span> <span class="p">{</span></span>
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4042
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<pre style="margin: 0;"> <span id="LC4042" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#ifdef SIXTY4_FORMAT</span></span>
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<pre style="margin: 0;">-<span id="LC4041" class="line" lang="cpp"> <span class="n" style="color: #333;">ebwtSide</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">new</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint64_t</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;">sideSz</span> <span class="o" style="font-weight: 600;">>></span> <span class="mi" style="color: #099;">3</span><span class="p"><span class="idiff right">]</span>;</span></span>
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4043
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<pre style="margin: 0;">+<span id="LC4043" class="line" lang="cpp"> <span class="n" style="color: #333;">ebwtSide</span><span class="p"><span class="idiff left">.</span></span><span class="n" style="color: #333;"><span class="idiff">resize</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;">sideSz</span> <span class="o" style="font-weight: 600;">>></span> <span class="mi" style="color: #099;">3</span><span class="p"><span class="idiff right">)</span>;</span></span>
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4044
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<pre style="margin: 0;"> <span id="LC4044" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#else</span></span>
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4043
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<pre style="margin: 0;">-<span id="LC4043" class="line" lang="cpp"> <span class="n" style="color: #333;">ebwtSide</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">new</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">uint8_t</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;">sideSz</span><span class="p"><span class="idiff right">]</span>;</span></span>
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4045
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<pre style="margin: 0;">+<span id="LC4045" class="line" lang="cpp"> <span class="n" style="color: #333;">ebwtSide</span><span class="p"><span class="idiff left">.</span></span><span class="n" style="color: #333;"><span class="idiff">resize</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;">sideSz</span><span class="p"><span class="idiff right">)</span>;</span></span>
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4046
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<pre style="margin: 0;"> <span id="LC4046" 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="LC4047" class="line" lang="cpp"></span>
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4048
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<pre style="margin: 0;"> <span id="LC4048" 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;">bad_alloc</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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4049
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<pre style="margin: 0;"> <span id="LC4049" 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;">"Out of memory allocating ebwtSide[] in "</span></span>
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4050
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<pre style="margin: 0;"> <span id="LC4050" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Ebwt::buildToDisk() at "</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;">":"</span></span>
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4051
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<pre style="margin: 0;"> <span id="LC4051" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">__LINE__</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="LC4052" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">throw</span> <span class="n" style="color: #333;">e</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC4053" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC4051" class="line" lang="cpp"> <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">ebwtSide</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="LC4054" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC4055" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Allocate a buffer to hold the ISA sample, which we accumulate in</span></span>
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<pre style="margin: 0;"> <span id="LC4056" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// the loop and then output at the end. We can't write output the</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4244" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -4244,7 +4246,7 @@ void Ebwt::buildToDisk(InorderBlockwiseSA<TStr>& sa,</td>
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4244
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4246
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<pre style="margin: 0;"> <span id="LC4246" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Write 'G' and 'T'</span></span>
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4245
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4247
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<pre style="margin: 0;"> <span id="LC4247" class="line" lang="cpp"> <span class="n" style="color: #333;">assert_leq</span><span class="p">(</span><span class="n" style="color: #333;">occSave</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">occ</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]);</span></span>
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4246
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4248
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<pre style="margin: 0;"> <span id="LC4248" class="line" lang="cpp"> <span class="n" style="color: #333;">assert_leq</span><span class="p">(</span><span class="n" style="color: #333;">occSave</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">],</span> <span class="n" style="color: #333;">occ</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]);</span></span>
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4247
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<pre style="margin: 0;">-<span id="LC4247" 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;">u32side</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">reinterpret_cast</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;">ebwtSide</span><span class="p">);</span></span>
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4249
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<pre style="margin: 0;">+<span id="LC4249" 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;">u32side</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">reinterpret_cast</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;">ebwtSide</span><span class="p"><span class="idiff left">.</span></span><span class="n" style="color: #333;"><span class="idiff">ptr</span></span><span class="p"><span class="idiff right">()</span>);</span></span>
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4248
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4250
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<pre style="margin: 0;"> <span id="LC4250" class="line" lang="cpp"> <span class="n" style="color: #333;">side</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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4249
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4251
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<pre style="margin: 0;"> <span id="LC4251" class="line" lang="cpp"> <span class="n" style="color: #333;">assert_leq</span><span class="p">(</span><span class="n" style="color: #333;">side</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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4250
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4252
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<pre style="margin: 0;"> <span id="LC4252" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#ifdef BOWTIE_64BIT_INDEX</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4255" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -4255,14 +4257,14 @@ void Ebwt::buildToDisk(InorderBlockwiseSA<TStr>& sa,</td>
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4255
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4257
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<pre style="margin: 0;"> <span id="LC4257" class="line" lang="cpp"> <span class="n" style="color: #333;">u32side</span><span class="p">[(</span><span class="n" style="color: #333;">sideSz</span> <span class="o" style="font-weight: 600;">>></span> <span class="mi" style="color: #099;">2</span><span class="p">)</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">endianizeU</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;">occSave</span><span class="p">[</span><span class="mi" style="color: #099;">1</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;">toBe</span><span class="p">());</span></span>
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4256
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4258
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<pre style="margin: 0;"> <span id="LC4258" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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4257
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4259
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<pre style="margin: 0;"> <span id="LC4259" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Write forward side to primary file</span></span>
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4258
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<pre style="margin: 0;">-<span id="LC4258" class="line" lang="cpp"> <span class="n" style="color: #333;">out1</span><span class="p">.</span><span class="n" style="color: #333;">write</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="p">)</span><span class="n" style="color: #333;">ebwtSide</span><span class="p">,</span> <span class="n" style="color: #333;">sideSz</span><span class="p">);</span></span>
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4260
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<pre style="margin: 0;">+<span id="LC4260" class="line" lang="cpp"> <span class="n" style="color: #333;">out1</span><span class="p">.</span><span class="n" style="color: #333;">write</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="p">)</span><span class="n" style="color: #333;">ebwtSide</span><span class="p"><span class="idiff left">.</span></span><span class="n" style="color: #333;"><span class="idiff">ptr</span></span><span class="p"><span class="idiff right">()</span>,</span> <span class="n" style="color: #333;">sideSz</span><span class="p">);</span></span>
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4259
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4261
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<pre style="margin: 0;"> <span id="LC4261" 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;">sideCur</span> <span class="o" style="font-weight: 600;">==</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="p">{</span></span>
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4260
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4262
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<pre style="margin: 0;"> <span id="LC4262" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Backward side boundary</span></span>
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4261
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4263
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<pre style="margin: 0;"> <span id="LC4263" 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;">si</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;">_sideBwtLen</span><span class="p">);</span></span>
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4262
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4264
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<pre style="margin: 0;"> <span id="LC4264" class="line" lang="cpp"> <span class="n" style="color: #333;">sideCur</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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4263
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4265
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<pre style="margin: 0;"> <span id="LC4265" class="line" lang="cpp"> <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">fw</span><span class="p">);</span> <span class="n" style="color: #333;">fw</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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4264
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4266
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<pre style="margin: 0;"> <span id="LC4266" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Write 'A' and 'C'</span></span>
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4265
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<pre style="margin: 0;">-<span id="LC4265" 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;">u32side</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">reinterpret_cast</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;">ebwtSide</span><span class="p">);</span></span>
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4267
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<pre style="margin: 0;">+<span id="LC4267" 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;">u32side</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">reinterpret_cast</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;">ebwtSide</span><span class="p"><span class="idiff left">.</span></span><span class="n" style="color: #333;"><span class="idiff">ptr</span></span><span class="p"><span class="idiff right">()</span>);</span></span>
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4266
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4268
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<pre style="margin: 0;"> <span id="LC4268" class="line" lang="cpp"> <span class="n" style="color: #333;">side</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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4267
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4269
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<pre style="margin: 0;"> <span id="LC4269" class="line" lang="cpp"> <span class="n" style="color: #333;">assert_leq</span><span class="p">(</span><span class="n" style="color: #333;">side</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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4268
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4270
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<pre style="margin: 0;"> <span id="LC4270" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#ifdef BOWTIE_64BIT_INDEX</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4275" style="width: 35px; color: rgba(0,0,0,0.3); 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="4277" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -4275,11 +4277,10 @@ void Ebwt::buildToDisk(InorderBlockwiseSA<TStr>& sa,</td>
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4275
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4277
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<pre style="margin: 0;"> <span id="LC4277" class="line" lang="cpp"> <span class="n" style="color: #333;">occSave</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;">occ</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">];</span> <span class="c1" style="color: #998; font-style: italic;">// save 'G' count</span></span>
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4276
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4278
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<pre style="margin: 0;"> <span id="LC4278" class="line" lang="cpp"> <span class="n" style="color: #333;">occSave</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;">occ</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">];</span> <span class="c1" style="color: #998; font-style: italic;">// save 'T' count</span></span>
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4277
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4279
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<pre style="margin: 0;"> <span id="LC4279" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Write backward side to primary file</span></span>
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4278
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<pre style="margin: 0;">-<span id="LC4278" class="line" lang="cpp"> <span class="n" style="color: #333;">out1</span><span class="p">.</span><span class="n" style="color: #333;">write</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="p">)</span><span class="n" style="color: #333;">ebwtSide</span><span class="p">,</span> <span class="n" style="color: #333;">sideSz</span><span class="p">);</span></span>
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4280
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<pre style="margin: 0;">+<span id="LC4280" class="line" lang="cpp"> <span class="n" style="color: #333;">out1</span><span class="p">.</span><span class="n" style="color: #333;">write</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="p">)</span><span class="n" style="color: #333;">ebwtSide</span><span class="p"><span class="idiff left">.</span></span><span class="n" style="color: #333;"><span class="idiff">ptr</span></span><span class="p"><span class="idiff right">()</span>,</span> <span class="n" style="color: #333;">sideSz</span><span class="p">);</span></span>
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4279
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4281
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<pre style="margin: 0;"> <span id="LC4281" class="line" lang="cpp"> <span class="p">}</span></span>
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4280
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4282
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<pre style="margin: 0;"> <span id="LC4282" class="line" lang="cpp"> <span class="p">}</span></span>
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4281
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4283
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<pre style="margin: 0;"> <span id="LC4283" class="line" lang="cpp"> <span class="n" style="color: #333;">VMSG_NL</span><span class="p">(</span><span class="s" style="color: #d14;">"Exited Ebwt loop"</span><span class="p">);</span></span>
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4282
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<pre style="margin: 0;">-<span id="LC4282" class="line" lang="cpp"> <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">ftab</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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4283
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4284
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<pre style="margin: 0;"> <span id="LC4284" class="line" lang="cpp"> <span class="n" style="color: #333;">assert_neq</span><span class="p">(</span><span class="n" style="color: #333;">zOff</span><span class="p">,</span> <span class="n" style="color: #333;">OFF_MASK</span><span class="p">);</span></span>
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4284
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4285
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<pre style="margin: 0;"> <span id="LC4285" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">absorbCnt</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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4285
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4286
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<pre style="margin: 0;"> <span id="LC4286" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Absorb any trailing, as-yet-unabsorbed short suffixes into</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4331" style="width: 35px; color: rgba(0,0,0,0.3); 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="4332" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -4331,20 +4332,20 @@ void Ebwt::buildToDisk(InorderBlockwiseSA<TStr>& sa,</td>
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4331
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4332
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<pre style="margin: 0;"> <span id="LC4332" class="line" lang="cpp"> <span class="p">}</span></span>
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4332
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4333
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<pre style="margin: 0;"> <span id="LC4333" class="line" lang="cpp"> <span class="n" style="color: #333;">assert_leq</span><span class="p">(</span><span class="n" style="color: #333;">eftabLen</span><span class="p">,</span> <span class="p">(</span><span class="n" style="color: #333;">TIndexOffU</span><span class="p">)</span><span class="n" style="color: #333;">eh</span><span class="p">.</span><span class="n" style="color: #333;">_ftabChars</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="LC4334" class="line" lang="cpp"> <span class="n" style="color: #333;">eftabLen</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;">_ftabChars</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="LC4334" class="line" lang="cpp"> <span class="n" style="color: #333;">TIndexOffU</span> <span class="o" style="font-weight: 600;"><span class="idiff left">*</span></span><span class="n" style="color: #333;">eftab</span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff right">NULL</span></span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC4335" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">EList</span></span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="n" style="color: #333;">TIndexOffU</span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span> <span class="n" style="color: #333;">eftab</span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">EBWT_CAT</span></span><span class="p"><span class="idiff right">)</span>;</span></span>
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<pre style="margin: 0;"> <span id="LC4336" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">try</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC4336" class="line" lang="cpp"> <span class="n" style="color: #333;">eftab</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">new</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">TIndexOffU</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;">eftabLen</span><span class="p"><span class="idiff right">]</span>;</span></span>
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4337
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<pre style="margin: 0;">-<span id="LC4337" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">memset</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">eftab</span></span><span class="p"><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">OFF_SIZE</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">eftabLen</span></span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC4337" class="line" lang="cpp"> <span class="n" style="color: #333;">eftab</span><span class="p"><span class="idiff left">.</span></span><span class="n" style="color: #333;"><span class="idiff">resize</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;">eftabLen</span><span class="p"><span class="idiff right">)</span>;</span></span>
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<pre style="margin: 0;">+<span id="LC4338" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">eftab</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">fillZero</span></span><span class="p"><span class="idiff right">(</span>);</span></span>
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<pre style="margin: 0;"> <span id="LC4339" 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;">bad_alloc</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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<pre style="margin: 0;"> <span id="LC4340" 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;">"Out of memory allocating eftab[] "</span></span>
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<pre style="margin: 0;"> <span id="LC4341" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"in Ebwt::buildToDisk() at "</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;">":"</span></span>
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<pre style="margin: 0;"> <span id="LC4342" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">__LINE__</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="LC4343" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">throw</span> <span class="n" style="color: #333;">e</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC4344" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC4344" class="line" lang="cpp"><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">assert</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">eftab</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">!=</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">NULL</span></span><span class="p"><span class="idiff right">);</span></span></span>
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<pre style="margin: 0;">+<span id="LC4345" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC4346" class="line" lang="cpp"> <span class="n" style="color: #333;">TIndexOffU</span> <span class="n" style="color: #333;">eftabCur</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="LC4347" 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;">1</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;">ftabLen</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="LC4347" class="line" lang="cpp"> <span class="n" style="color: #333;">TIndexOffU</span> <span class="n" style="color: #333;">lo</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ftab</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;">Ebwt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ftabHi</span><span class="p">(</span><span class="n" style="color: #333;">ftab</span><span class="p">,</span> <span class="n" style="color: #333;">eftab</span><span class="p">,</span> <span class="n" style="color: #333;">len</span><span class="p">,</span> <span class="n" style="color: #333;">ftabLen</span><span class="p">,</span> <span class="n" style="color: #333;">eftabLen</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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<pre style="margin: 0;">+<span id="LC4348" class="line" lang="cpp"> <span class="n" style="color: #333;">TIndexOffU</span> <span class="n" style="color: #333;">lo</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ftab</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;">Ebwt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ftabHi</span><span class="p">(</span><span class="n" style="color: #333;">ftab</span><span class="p"><span class="idiff left">.</span></span><span class="n" style="color: #333;"><span class="idiff">ptr</span></span><span class="p"><span class="idiff">()</span>,</span> <span class="n" style="color: #333;">eftab</span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">ptr</span></span><span class="p"><span class="idiff right">()</span>,</span> <span class="n" style="color: #333;">len</span><span class="p">,</span> <span class="n" style="color: #333;">ftabLen</span><span class="p">,</span> <span class="n" style="color: #333;">eftabLen</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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4349
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<pre style="margin: 0;"> <span id="LC4349" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">absorbFtab</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC4350" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Skip a number of short pattern indicated by absorbFtab[i]</span></span>
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4351
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<pre style="margin: 0;"> <span id="LC4351" class="line" lang="cpp"> <span class="n" style="color: #333;">TIndexOffU</span> <span class="n" style="color: #333;">hi</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">lo</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">absorbFtab</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -4352,13 +4353,13 @@ void Ebwt::buildToDisk(InorderBlockwiseSA<TStr>& sa,</td>
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<pre style="margin: 0;"> <span id="LC4353" class="line" lang="cpp"> <span class="n" style="color: #333;">eftab</span><span class="p">[</span><span class="n" style="color: #333;">eftabCur</span><span class="o" style="font-weight: 600;">*</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">lo</span><span class="p">;</span></span>
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4354
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<pre style="margin: 0;"> <span id="LC4354" class="line" lang="cpp"> <span class="n" style="color: #333;">eftab</span><span class="p">[</span><span class="n" style="color: #333;">eftabCur</span><span class="o" style="font-weight: 600;">*</span><span class="mi" style="color: #099;">2</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">hi</span><span class="p">;</span></span>
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4354
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4355
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<pre style="margin: 0;"> <span id="LC4355" class="line" lang="cpp"> <span class="n" style="color: #333;">ftab</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="p">(</span><span class="n" style="color: #333;">eftabCur</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;">OFF_MASK</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// insert pointer into eftab</span></span>
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<pre style="margin: 0;">-<span id="LC4355" class="line" lang="cpp"> <span class="n" style="color: #333;">assert_eq</span><span class="p">(</span><span class="n" style="color: #333;">lo</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;">ftabLo</span><span class="p">(</span><span class="n" style="color: #333;">ftab</span><span class="p">,</span> <span class="n" style="color: #333;">eftab</span><span class="p">,</span> <span class="n" style="color: #333;">len</span><span class="p">,</span> <span class="n" style="color: #333;">ftabLen</span><span class="p">,</span> <span class="n" style="color: #333;">eftabLen</span><span class="p">,</span> <span class="n" style="color: #333;">i</span><span class="p">));</span></span>
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4356
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<pre style="margin: 0;">-<span id="LC4356" class="line" lang="cpp"> <span class="n" style="color: #333;">assert_eq</span><span class="p">(</span><span class="n" style="color: #333;">hi</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;">ftabHi</span><span class="p">(</span><span class="n" style="color: #333;">ftab</span><span class="p">,</span> <span class="n" style="color: #333;">eftab</span><span class="p">,</span> <span class="n" style="color: #333;">len</span><span class="p">,</span> <span class="n" style="color: #333;">ftabLen</span><span class="p">,</span> <span class="n" style="color: #333;">eftabLen</span><span class="p">,</span> <span class="n" style="color: #333;">i</span><span class="p">));</span></span>
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<pre style="margin: 0;">+<span id="LC4356" class="line" lang="cpp"> <span class="n" style="color: #333;">assert_eq</span><span class="p">(</span><span class="n" style="color: #333;">lo</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;">ftabLo</span><span class="p">(</span><span class="n" style="color: #333;">ftab</span><span class="p"><span class="idiff left">.</span></span><span class="n" style="color: #333;"><span class="idiff">ptr</span></span><span class="p"><span class="idiff">()</span>,</span> <span class="n" style="color: #333;">eftab</span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">ptr</span></span><span class="p"><span class="idiff right">()</span>,</span> <span class="n" style="color: #333;">len</span><span class="p">,</span> <span class="n" style="color: #333;">ftabLen</span><span class="p">,</span> <span class="n" style="color: #333;">eftabLen</span><span class="p">,</span> <span class="n" style="color: #333;">i</span><span class="p">));</span></span>
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<pre style="margin: 0;">+<span id="LC4357" class="line" lang="cpp"> <span class="n" style="color: #333;">assert_eq</span><span class="p">(</span><span class="n" style="color: #333;">hi</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;">ftabHi</span><span class="p">(</span><span class="n" style="color: #333;">ftab</span><span class="p"><span class="idiff left">.</span></span><span class="n" style="color: #333;"><span class="idiff">ptr</span></span><span class="p"><span class="idiff">()</span>,</span> <span class="n" style="color: #333;">eftab</span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">ptr</span></span><span class="p"><span class="idiff right">()</span>,</span> <span class="n" style="color: #333;">len</span><span class="p">,</span> <span class="n" style="color: #333;">ftabLen</span><span class="p">,</span> <span class="n" style="color: #333;">eftabLen</span><span class="p">,</span> <span class="n" style="color: #333;">i</span><span class="p">));</span></span>
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<pre style="margin: 0;"> <span id="LC4358" 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="LC4359" class="line" lang="cpp"> <span class="n" style="color: #333;">ftab</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;">lo</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC4360" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC4361" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC4361" class="line" lang="cpp"> <span class="n" style="color: #333;">assert_eq</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;">ftabHi</span><span class="p">(</span><span class="n" style="color: #333;">ftab</span><span class="p">,</span> <span class="n" style="color: #333;">eftab</span><span class="p">,</span> <span class="n" style="color: #333;">len</span><span class="p">,</span> <span class="n" style="color: #333;">ftabLen</span><span class="p">,</span> <span class="n" style="color: #333;">eftabLen</span><span class="p">,</span> <span class="n" style="color: #333;">ftabLen</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;">len</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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4362
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<pre style="margin: 0;">+<span id="LC4362" class="line" lang="cpp"> <span class="n" style="color: #333;">assert_eq</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;">ftabHi</span><span class="p">(</span><span class="n" style="color: #333;">ftab</span><span class="p"><span class="idiff left">.</span></span><span class="n" style="color: #333;"><span class="idiff">ptr</span></span><span class="p"><span class="idiff">()</span>,</span> <span class="n" style="color: #333;">eftab</span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">ptr</span></span><span class="p"><span class="idiff right">()</span>,</span> <span class="n" style="color: #333;">len</span><span class="p">,</span> <span class="n" style="color: #333;">ftabLen</span><span class="p">,</span> <span class="n" style="color: #333;">eftabLen</span><span class="p">,</span> <span class="n" style="color: #333;">ftabLen</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;">len</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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4362
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4363
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<pre style="margin: 0;"> <span id="LC4363" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Write ftab to primary file</span></span>
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4364
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<pre style="margin: 0;"> <span id="LC4364" 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;">ftabLen</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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4365
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<pre style="margin: 0;"> <span id="LC4365" 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="n" style="color: #333;">ftab</span><span class="p">[</span><span class="n" style="color: #333;">i</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;">toBe</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">@@ -4379,9 +4380,6 @@ void Ebwt::buildToDisk(InorderBlockwiseSA<TStr>& sa,</td>
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<pre style="margin: 0;"> <span id="LC4380" class="line" lang="cpp"> <span class="p">}</span></span>
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4381
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<pre style="margin: 0;"> <span id="LC4381" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">delete</span><span class="p">[]</span> <span class="n" style="color: #333;">isaSample</span><span class="p">;</span></span>
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4382
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<pre style="margin: 0;"> <span id="LC4382" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC4382" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">delete</span><span class="p">[]</span> <span class="n" style="color: #333;">ftab</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC4383" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">delete</span><span class="p">[]</span> <span class="n" style="color: #333;">eftab</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC4384" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">delete</span><span class="p">[]</span> <span class="n" style="color: #333;">absorbFtab</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC4383" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC4384" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Note: if you'd like to sanity-check the Ebwt, you'll have to</span></span>
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<pre style="margin: 0;"> <span id="LC4385" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// read it back into memory first!</span></span>
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<a href="https://salsa.debian.org/med-team/bowtie/-/compare/fb3a91ce60d73bf653156f07370b7b34ba81ad97...9bf017434a90cf99f756c6ce9e222a7ed0c86a44#69652f4e3eff95542ec1637fffb5d028d18a5a54"><strong>ebwt_search_util.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">@@ -34,7 +34,7 @@ struct QueryMutation {</td>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * into the spillover list, a non-tail entry in the spillover list, or</span></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * a tail entry in the spillover list.</span></span>
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<pre style="margin: 0;"> <span id="LC36" 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="LC37" class="line" lang="cpp"><span class="k" style="font-weight: 600;">typedef</span> <span class="k" style="font-weight: 600;">union</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="cpp"><span class="k" style="font-weight: 600;">typedef</span> <span class="k" style="font-weight: 600;">union</span> <span class="n" style="color: #333;"><span class="idiff left">PartialAlignment</span></span><span class="idiff right"> </span><span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">struct</span> <span class="p">{</span></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;">uint64_t</span> <span class="n" style="color: #333;">pos0</span> <span class="o" style="font-weight: 600;">:</span> <span class="mi" style="color: #099;">16</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// mismatched pos 1</span></span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">pos1</span> <span class="o" style="font-weight: 600;">:</span> <span class="mi" style="color: #099;">16</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// mismatched pos 2</span></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">NC_008253.bfa</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">@@ -288,16 +288,21 @@ public:</td>
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<pre style="margin: 0;"> <span id="LC288" class="line" lang="cpp"> <span class="n" style="color: #333;">numMaxed</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">ptNumMaxed_</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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<pre style="margin: 0;"> <span id="LC289" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC290" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC291" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">tot</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">numAligned</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">numUnaligned</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">numMaxed</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC291" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">tot</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">numAligned</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">numUnaligned</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC292" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">sampleMax_</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC293" class="line" lang="cpp"> <span class="n" style="color: #333;">tot</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">numMaxed</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC294" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">alPct</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">0.0</span><span class="p">,</span> <span class="n" style="color: #333;">unalPct</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">0.0</span><span class="p">,</span> <span class="n" style="color: #333;">maxPct</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">0.0</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC295" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">tot</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="LC294" class="line" lang="cpp"> <span class="n" style="color: #333;">alPct</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">100.0</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)(</span><span class="n" style="color: #333;">numAligned</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">numMaxed</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)</span><span class="n" style="color: #333;">tot</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC296" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">sampleMax_</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC297" class="line" lang="cpp"> <span class="n" style="color: #333;">alPct</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">100.0</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)(</span><span class="n" style="color: #333;">numAligned</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)</span><span class="n" style="color: #333;">tot</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC298" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span></span>
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<pre style="margin: 0;">+<span id="LC299" class="line" lang="cpp"> <span class="n" style="color: #333;">alPct</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">100.0</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)(</span><span class="n" style="color: #333;">numAligned</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">numMaxed</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)</span><span class="n" style="color: #333;">tot</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC300" class="line" lang="cpp"> <span class="n" style="color: #333;">unalPct</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">100.0</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)</span><span class="n" style="color: #333;">numUnaligned</span> <span class="o" style="font-weight: 600;">/</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)</span><span class="n" style="color: #333;">tot</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC301" class="line" lang="cpp"> <span class="n" style="color: #333;">maxPct</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">100.0</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)</span><span class="n" style="color: #333;">numMaxed</span> <span class="o" style="font-weight: 600;">/</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)</span><span class="n" style="color: #333;">tot</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC302" class="line" lang="cpp"> <span class="p">}</span></span>
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298
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<pre style="margin: 0;"> <span id="LC303" 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;">"# reads processed: "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">tot</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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299
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304
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<pre style="margin: 0;"> <span id="LC304" 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;">"# reads with at least one alignment: "</span></span>
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<pre style="margin: 0;">-<span id="LC300" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">numAligned</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">numMaxed</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;">fixed</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">setprecision</span><span class="p">(</span><span class="mi" style="color: #099;">2</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC305" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">numAligned</span> <span class="o" style="font-weight: 600;">+</span> <span class="p"><span class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">sampleMax_</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="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">:</span></span><span class="idiff"> </span><span class="n" style="color: #333;">numMaxed</span><span class="p"><span class="idiff right">)</span></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;">fixed</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">setprecision</span><span class="p">(</span><span class="mi" style="color: #099;">2</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC306" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">alPct</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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302
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<pre style="margin: 0;"> <span id="LC307" 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;">"# reads that failed to align: "</span></span>
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308
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<pre style="margin: 0;"> <span id="LC308" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">numUnaligned</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;">fixed</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">setprecision</span><span class="p">(</span><span class="mi" style="color: #099;">2</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">@@ -770,7 +775,6 @@ public:</td>
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775
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<pre style="margin: 0;"> <span id="LC775" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">paired</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC776" class="line" lang="cpp"> <span class="n" style="color: #333;">xms</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="LC777" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC773" class="line" lang="cpp"> <span class="n" style="color: #333;">xms</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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778
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<pre style="margin: 0;"> <span id="LC778" class="line" lang="cpp"> <span class="n" style="color: #333;">_sink</span><span class="p">.</span><span class="n" style="color: #333;">reportHits</span><span class="p">(</span><span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">_bufferedHits</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">_bufferedHits</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="LC779" class="line" lang="cpp"> <span class="n" style="color: #333;">threadId_</span><span class="p">,</span> <span class="n" style="color: #333;">mapq</span><span class="p">,</span> <span class="n" style="color: #333;">xms</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">,</span> <span class="n" style="color: #333;">p</span><span class="p">);</span></span>
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780
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<pre style="margin: 0;"> <span id="LC780" class="line" lang="cpp"> <span class="n" style="color: #333;">_sink</span><span class="p">.</span><span class="n" style="color: #333;">dumpAlign</span><span class="p">(</span><span class="n" style="color: #333;">p</span><span class="p">);</span></span>
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<a href="https://salsa.debian.org/med-team/bowtie/-/compare/fb3a91ce60d73bf653156f07370b7b34ba81ad97...9bf017434a90cf99f756c6ce9e222a7ed0c86a44#88d2b0f7968c3acf1acde0c4814002d780087895"><strong>mem_ids.h</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/*</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * Copyright 2011, Ben Langmead <langmea@cs.jhu.edu></span></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * This file is part of Bowtie 2.</span></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * Bowtie 2 is free software: you can redistribute it and/or modify</span></span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * it under the terms of the GNU General Public License as published by</span></span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * the Free Software Foundation, either version 3 of the License, or</span></span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * (at your option) any later version.</span></span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * Bowtie 2 is distributed in the hope that it will be useful,</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * but WITHOUT ANY WARRANTY; without even the implied warranty of</span></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the</span></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * GNU General Public License for more details.</span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * You should have received a copy of the GNU General Public License</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * along with Bowtie 2. If not, see <http://www.gnu.org/licenses/>.</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// For holding index data</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define EBWT_CAT ((int) 1)</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// For holding index-building data</span></span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define EBWTB_CAT ((int) 2)</span></span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// For holding cache data</span></span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define CA_CAT ((int) 3)</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// For holding group-walk-left bookkeeping data</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define GW_CAT ((int) 4)</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// For holding alignment bookkeeping data</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define AL_CAT ((int) 5)</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// For holding dynamic programming bookkeeping data</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define DP_CAT ((int) 6)</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// For holding alignment results and other hit objects</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define RES_CAT ((int) 7)</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define MISC_CAT ((int) 9)</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define DEBUG_CAT ((int)10)</span></span></pre>
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<a href="https://salsa.debian.org/med-team/bowtie/-/compare/fb3a91ce60d73bf653156f07370b7b34ba81ad97...9bf017434a90cf99f756c6ce9e222a7ed0c86a44#d29fd14304274912c3f57246f6c1ac7e34eab154"><strong>multikey_qsort.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 MULTIKEY_QSORT_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 MULTIKEY_QSORT_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 <algorithm></span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <iostream></span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "alphabet.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">@@ -292,26 +293,38 @@ bool assertPartitionedSuf2(</td>
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<pre style="margin: 0;"> <span id="LC293" 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="LC294" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC295" 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="LC295" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Assert that <span class="idiff left">the seqan::S</span>tring s of suffix offsets into s<span class="idiff right">eqan::Str</span>ing</span></span>
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<pre style="margin: 0;">-<span id="LC296" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * <span class="idiff left right">'host' is a seemingly </span>legitimate suffix-offset list (at this time,</span></span>
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297
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<pre style="margin: 0;">-<span id="LC297" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * <span class="idiff left right">we just check that it doesn't </span>list any suffix twice).</span></span>
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<pre style="margin: 0;">+<span id="LC296" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Assert that <span class="idiff left">s</span>tring s of suffix offsets into s<span class="idiff">tring 'host' is a seem</span>ing<span class="idiff right">ly</span></span></span>
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<pre style="margin: 0;">+<span id="LC297" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * legitimate suffix-offset list (at this time,<span class="idiff left right"> we just check that it doesn't</span></span></span>
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<pre style="margin: 0;">+<span id="LC298" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * list any suffix twice).</span></span>
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<pre style="margin: 0;"> <span id="LC299" 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="LC300" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC301" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kr" style="font-weight: 600;">inline</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">sanityCheckInputSufs</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;">s</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">slen</span><span class="p">)</span> <span class="p">{</span></span>
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302
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<pre style="margin: 0;"> <span id="LC302" class="line" lang="cpp"> <span class="n" style="color: #333;">assert_gt</span><span class="p">(</span><span class="n" style="color: #333;">slen</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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301
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<pre style="margin: 0;">-<span id="LC301" 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;">slen</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="LC302" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Actually, it's convenient to allow the caller to provide</span></span>
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<pre style="margin: 0;">-<span id="LC303" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// suffix offsets thare are off the end of the host string.</span></span>
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<pre style="margin: 0;">-<span id="LC304" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// See, e.g., build() in diff_sample.cpp.</span></span>
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<pre style="margin: 0;">-<span id="LC305" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//assert_lt(s[i], length(host));</span></span>
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<pre style="margin: 0;">-<span id="LC306" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="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 class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">slen</span><span class="p">;</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC307" class="line" lang="cpp"> <span class="n" style="color: #333;">assert_neq</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">],</span> <span class="n" style="color: #333;">s</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]);</span></span>
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<pre style="margin: 0;">+<span id="LC303" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Try keeping the running time <1min</span></span>
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<pre style="margin: 0;">+<span id="LC304" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">slen</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">4096</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC305" 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;">s_copy</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">TIndexOffU</span><span class="p">[</span><span class="n" style="color: #333;">slen</span><span class="p">];</span></span>
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<pre style="margin: 0;">+<span id="LC306" class="line" lang="cpp"> <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">s_copy</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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307
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<pre style="margin: 0;">+<span id="LC307" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">copy</span><span class="p">(</span><span class="n" style="color: #333;">s</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;">slen</span><span class="p">,</span> <span class="n" style="color: #333;">s_copy</span><span class="p">);</span></span>
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308
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<pre style="margin: 0;">+<span id="LC308" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">sort</span><span class="p">(</span><span class="n" style="color: #333;">s_copy</span><span class="p">,</span> <span class="n" style="color: #333;">s_copy</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">slen</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC309" 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;">slen</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>
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<pre style="margin: 0;">+<span id="LC310" class="line" lang="cpp"> <span class="n" style="color: #333;">assert_neq</span><span class="p">(</span><span class="n" style="color: #333;">s_copy</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">],</span> <span class="n" style="color: #333;">s_copy</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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311
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<pre style="margin: 0;">+<span id="LC311" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">delete</span><span class="p">[]</span> <span class="n" style="color: #333;">s_copy</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC312" 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="LC313" 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;">slen</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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314
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<pre style="margin: 0;">+<span id="LC314" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Actually, it's convenient to allow the caller to provide</span></span>
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315
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<pre style="margin: 0;">+<span id="LC315" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// suffix offsets thare are off the end of the host string.</span></span>
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316
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<pre style="margin: 0;">+<span id="LC316" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// See, e.g., build() in diff_sample.cpp.</span></span>
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317
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<pre style="margin: 0;">+<span id="LC317" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//assert_lt(s[i], length(host));</span></span>
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318
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<pre style="margin: 0;">+<span id="LC318" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="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 class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">slen</span><span class="p">;</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC319" class="line" lang="cpp"> <span class="n" style="color: #333;">assert_neq</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">],</span> <span class="n" style="color: #333;">s</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]);</span></span>
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<pre style="margin: 0;">+<span id="LC320" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC321" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC322" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC323" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC324" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC325" 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="LC313" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Assert that the s<span class="idiff left">eqan::S</span>tring s of suffix offsets into <span class="idiff">seqan::Str</span>in<span class="idiff right">g</span></span></span>
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314
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<pre style="margin: 0;">-<span id="LC314" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * <span class="idiff left right">'host' really are in </span>lexicographical order up to depth 'upto'.</span></span>
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326
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<pre style="margin: 0;">+<span id="LC326" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Assert that the string s of suffix offsets into <span class="idiff left right"> 'host' really are </span>in</span></span>
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<pre style="margin: 0;">+<span id="LC327" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * lexicographical order up to depth 'upto'.</span></span>
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315
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328
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<pre style="margin: 0;"> <span id="LC328" 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="LC329" 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="LC330" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">sanityCheckOrderedSufs</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">T</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">host</span><span class="p">,</span></span>
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<a href="https://salsa.debian.org/med-team/bowtie/-/compare/fb3a91ce60d73bf653156f07370b7b34ba81ad97...9bf017434a90cf99f756c6ce9e222a7ed0c86a44#cc60758ea89135534b00a4c0ae3e29ee95c0ef25"><strong>scripts/bowtie-hbb.sh</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">@@ -44,7 +44,17 @@ fi</td>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># this variant creates static binaries with PIC</span></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="shell"><span class="nb" style="color: #0086b3;">source</span> /hbb_exe_gc_hardened/activate</span>
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46
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="shell">make bowtie-bin.zip</span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="shell"><span class="nb" style="color: #0086b3;">mkdir</span> /mybin</span>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s1" style="color: #d14;">'res=`echo $@ | sed "s/-L.*$//"`; /opt/rh/devtoolset-8/root/usr/bin/ar $res;'</span> <span class="o" style="font-weight: 600;">></span> /mybin/ar</span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="shell"><span class="nb" style="color: #0086b3;">chmod</span> +x /mybin/ar <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">export </span><span class="nv" style="color: #008080;">PATH</span><span class="o" style="font-weight: 600;">=</span>/mybin:<span class="nv" style="color: #008080;">$PATH</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># make static-libs</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># if [ $? -ne 0 ] ; then</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># echo "Unable to build tbb and/or zlib static dependencies"</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># exit 1</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># fi</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="shell">make bowtie-bin.zip <span class="nv" style="color: #008080;">RELEASE_BUILD</span><span class="o" style="font-weight: 600;">=</span>1</span>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nv" style="color: #008080;">$?</span> <span class="nt" style="color: #000080;">-ne</span> 0 <span class="o" style="font-weight: 600;">]</span> <span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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49
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Unable to create bowtie package"</span></span>
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50
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">exit </span>1</span>
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<a href="https://salsa.debian.org/med-team/bowtie/-/compare/fb3a91ce60d73bf653156f07370b7b34ba81ad97...9bf017434a90cf99f756c6ce9e222a7ed0c86a44#1ba32b1a76b5b57a56e4d834114b45c9fbeb218e"><strong>shmem.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">@@ -10,6 +10,7 @@</td>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#ifdef BOWTIE_SHARED_MEM</span></span>
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12
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <iostream></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 <string></span></span>
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15
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <sys/shm.h></span></span>
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16
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <unistd.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">@@ -102,7 +103,7 @@ bool allocSharedMem(std::string fname,</td>
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102
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103
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="cpp"> <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"shmctl returned "</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="s" style="color: #d14;">" for IPC_STAT and errno is "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">errno</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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103
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104
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<pre style="margin: 0;"> <span id="LC104" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">throw</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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104
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105
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<pre style="margin: 0;"> <span id="LC105" class="line" lang="cpp"> <span class="p">}</span></span>
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105
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<pre style="margin: 0;">-<span id="LC105" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">ds</span><span class="p">.</span><span class="n" style="color: #333;">shm_segsz</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">shmemLen</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;">if</span><span class="p">(<span class="idiff left">(</span></span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">size_t</span></span><span class="p"><span class="idiff right">)</span></span><span class="n" style="color: #333;">ds</span><span class="p">.</span><span class="n" style="color: #333;">shm_segsz</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">shmemLen</span><span class="p">)</span> <span class="p">{</span></span>
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106
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107
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<pre style="margin: 0;"> <span id="LC107" class="line" lang="cpp"> <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Warning: shared-memory chunk's segment size ("</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">ds</span><span class="p">.</span><span class="n" style="color: #333;">shm_segsz</span></span>
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107
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108
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<pre style="margin: 0;"> <span id="LC108" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">") doesn't match expected size ("</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">shmemLen</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>
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108
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109
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<pre style="margin: 0;"> <span id="LC109" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Deleting old shared memory block and trying again."</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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<a href="https://salsa.debian.org/med-team/bowtie/-/compare/fb3a91ce60d73bf653156f07370b7b34ba81ad97...9bf017434a90cf99f756c6ce9e222a7ed0c86a44#660ce3632dfae6bcb8dd9430bc227c1af48265ec"><strong>threading.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">@@ -19,13 +19,17 @@</td>
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19
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#ifdef NO_SPINLOCK</span></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"># if (__cplusplus >= 201103L)</span></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"># ifdef WITH_QUEUELOCK</span></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="cpp"><span class="idiff left"> </span> <span class="cp" style="color: #999; font-weight: 600;"><span class="idiff right">#</span>include "bt2_locks.h"</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;"># <span class="idiff left right"> </span>define MUTEX_T mcs_lock</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"><span class="idiff left right">#</span> include "bt2_locks.h"</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;"># <span class="idiff left right"> </span>define MUTEX_T mcs_lock</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;"># else</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;"># <span class="idiff left right"> </span>define MUTEX_T std::mutex</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;"># define MUTEX_T std::mutex</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;"># endif</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;"># else</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;"># define MUTEX_T tthread::mutex</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;"># ifdef WITH_QUEUELOCK</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"># error "QUEUELOCK requires C++11 or newer."</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"># else</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;"># define MUTEX_T tthread::mutex</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;"># endif</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;"># endif</span></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#else</span></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"># if (__cplusplus >= 201103L)</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">@@ -57,24 +61,56 @@ struct thread_tracking_pair {</td>
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<pre style="margin: 0;"> <span id="LC61" 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="LC62" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Wrap a lock; obtain lock upon construction, release upon destruction.</span></span>
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<pre style="margin: 0;"> <span id="LC63" 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="LC64" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// class ThreadSafe {</span></span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// public:</span></span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// ThreadSafe(MUTEX_T* ptr_mutex) :</span></span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// ptr_mutex_(ptr_mutex)</span></span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// {</span></span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// assert(ptr_mutex_ != NULL);</span></span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// ptr_mutex_->lock();</span></span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// }</span></span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// ~ThreadSafe() {</span></span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// ptr_mutex_->unlock();</span></span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// }</span></span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// private:</span></span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// MUTEX_T *ptr_mutex_;</span></span>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// };</span></span>
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="cpp"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">ThreadSafe</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="cpp"><span class="nl">public:</span></span>
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83
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="cpp"> <span class="n" style="color: #333;">ThreadSafe</span><span class="p">(</span><span class="n" style="color: #333;">MUTEX_T</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">ptr_mutex</span><span class="p">)</span> <span class="o" style="font-weight: 600;">:</span></span>
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64
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="cpp"> <span class="n" style="color: #333;">ptr_mutex_</span><span class="p">(</span><span class="n" style="color: #333;">ptr_mutex</span><span class="p">)</span></span>
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65
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="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="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">ptr_mutex_</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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67
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="cpp"> <span class="n" style="color: #333;">ptr_mutex_</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">lock</span><span class="p">();</span></span>
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68
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<pre style="margin: 0;">-<span id="LC68" class="line" lang="cpp"> <span 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;">ThreadSafe</span><span class="p">(</span><span class="n" style="color: #333;">MUTEX_T</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">mutex</span><span class="p">)</span> <span class="o" style="font-weight: 600;">:</span></span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#if (__cplusplus >= 201103L && defined(NO_SPINLOCK) && defined(WITH_QUEUELOCK))</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;">node_</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="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="cpp"> <span class="n" style="color: #333;">mutex_</span><span class="p">(</span><span class="n" style="color: #333;">mutex</span><span class="p">)</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="cp" style="color: #999; font-weight: 600;">#if (__cplusplus >= 201103L && defined(NO_SPINLOCK) && defined(WITH_QUEUELOCK))</span></span>
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="cpp"> <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;">node_</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#else</span></span>
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="cpp"> <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>
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<pre style="margin: 0;">+<span id="LC93" 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="LC94" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC96" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC97" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">~</span><span class="n" style="color: #333;">ThreadSafe</span><span class="p">()</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="cpp"> <span class="n" style="color: #333;">ptr_mutex_</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">unlock</span><span class="p">();</span></span>
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#if (__cplusplus >= 201103L && defined(NO_SPINLOCK) && defined(WITH_QUEUELOCK))</span></span>
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="cpp"> <span class="n" style="color: #333;">mutex_</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">unlock</span><span class="p">(</span><span class="n" style="color: #333;">node_</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#else</span></span>
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="cpp"> <span class="n" style="color: #333;">mutex_</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">unlock</span><span class="p">();</span></span>
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<pre style="margin: 0;">+<span id="LC102" 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="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="nl">private:</span></span>
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<pre style="margin: 0;">-<span id="LC75" class="line" lang="cpp"> <span class="n" style="color: #333;">MUTEX_T</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">ptr_mutex_</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>
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#if (__cplusplus >= 201103L && defined(NO_SPINLOCK) && defined(WITH_QUEUELOCK))</span></span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="cpp"> <span class="n" style="color: #333;">MUTEX_T</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">mcs_node</span> <span class="n" style="color: #333;">node_</span><span class="p">;</span></span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="cpp"> <span class="n" style="color: #333;">MUTEX_T</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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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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<pre style="margin: 0;"> <span id="LC112" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC114" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#if defined(_TTHREAD_WIN32_)</span></span>
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<pre style="margin: 0;"> <span id="LC115" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#define SLEEP(x) Sleep(x)</span></span>
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<pre style="margin: 0;"> <span id="LC116" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#else</span></span>
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<a href="https://salsa.debian.org/med-team/bowtie/-/compare/fb3a91ce60d73bf653156f07370b7b34ba81ad97...9bf017434a90cf99f756c6ce9e222a7ed0c86a44#26207b119752bd3d9fe20ed0efc42bec280de0eb"><strong>tinythread.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">@@ -21,6 +21,8 @@ freely, subject to the following restrictions:</td>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> distribution.</span></span>
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<pre style="margin: 0;"> <span id="LC22" 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="LC23" class="line" lang="cpp"></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;">#if (__cplusplus < 201103L)</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="cpp"></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 <exception></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 "tinythread.h"</span></span>
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<pre style="margin: 0;"> <span id="LC28" 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">@@ -301,3 +303,5 @@ thread::id this_thread::get_id()</td>
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<pre style="margin: 0;"> <span id="LC303" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC304" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC305" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC306" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC307" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span></pre>
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<a href="https://salsa.debian.org/med-team/bowtie/-/compare/fb3a91ce60d73bf653156f07370b7b34ba81ad97...9bf017434a90cf99f756c6ce9e222a7ed0c86a44#54b33722b92cc6ac990c217292b257c08318a6a5"><strong>util.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">@@ -47,7 +47,7 @@ char* itoa10(const T& value, char* result) {</td>
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47
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Only apply negative sign for base 10</span></span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</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;">numeric_limits</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;">is_signed</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Avoid compiler warning in cases where T is unsigned</span></span>
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">value</span> <span class="o" style="font-weight: 600;"><<span class="idiff left">=</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">0</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">value</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff right">!=</span></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;">out</span><span class="o" style="font-weight: 600;">++</span> <span class="o" style="font-weight: 600;">=</span> <span class="sc" style="color: #d14;">'-'</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">value</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;">out</span><span class="o" style="font-weight: 600;">++</span> <span class="o" style="font-weight: 600;">=</span> <span class="sc" style="color: #d14;">'-'</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">reverse</span><span class="p">(</span> <span class="n" style="color: #333;">result</span><span class="p">,</span> <span class="n" style="color: #333;">out</span> <span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">out</span> <span class="o" style="font-weight: 600;">=</span> <span class="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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