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GitLab

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<h3>

Sascha Steinbiss pushed to branch upstream

at <a href="https://salsa.debian.org/med-team/mash">Debian Med / mash</a>

</h3>

<h4>

Commits:

</h4>

<ul>

<li>

<strong><a href="https://salsa.debian.org/med-team/mash/commit/5e14db80cf1008378399b328c70a9ff7b5c730e4">5e14db80</a></strong>

<div>

<span>by Sascha Steinbiss</span>

<i>at 2019-07-31T13:48:06Z</i>

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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2.2+dfsg</pre>

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<h4>13 changed files:</h4>

<ul>

<li class="file-stats">

<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">

README.md

</a>

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<li class="file-stats">

<a href="#10c9d422887ff3796fa73258e801014a688c7a49">

doc/sphinx/conf.py

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<a href="#095583c2a50662366c7d4714646e3178e4673738">

doc/sphinx/data.rst

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<li class="file-stats">

<a href="#5a765931f4b88491a9e9eb9822872702c171539c">

doc/sphinx/index.rst

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<li class="file-stats">

<a href="#1b90382419cff5ed5a17e0b2bebbff0c68ecadae">

src/mash/CommandBounds.cpp

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<a href="#2fffcd35413c3c60b76498e1abc911123672535d">

src/mash/CommandDistance.cpp

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<a href="#d36a6e2bfbbc612f16d6ba17bf5feb1f1e7100e0">

src/mash/CommandDistance.h

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<li class="file-stats">

<a href="#b1869287016c57e645de15f0b9ede057292d44b7">

src/mash/CommandScreen.cpp

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<a href="#c1907300070128758e5df535932ad22cf1b51bf9">

src/mash/CommandScreen.h

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<a href="#e8b45cfb4cd2406e50d5c27273b019116a793f02">

src/mash/CommandTriangle.cpp

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<a href="#d02e98b4956e5520d320ab853dea3fc999d68ce8">

src/mash/CommandTriangle.h

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<a href="#2ecd5edfb9906ffd092b9b8b4d28f6cb2eed2783">

src/mash/version.h

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<a href="#73531968fb1b31378d10ac3f11bf38fff6f7028c">

test/ref/screen

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<h4>Changes:</h4>

<li id="8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">

<a href="https://salsa.debian.org/med-team/mash/commit/5e14db80cf1008378399b328c70a9ff7b5c730e4#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d"><strong>README.md</strong></a>

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<pre style="margin: 0;"> <span id="LC1" class="line" lang="markdown">Mash is normally distributed as a dependency-free binary for Linux or OSX (see</span>

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<pre style="margin: 0;"> <span id="LC2" class="line" lang="markdown">https://github.com/marbl/Mash/releases). This source distribution is intended</span>

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<pre style="margin: 0;">-<span id="LC3" class="line" lang="markdown">for other operating systems or for development. Mash requires c++1<span class="idiff left right">1</span> to build,</span>

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<pre style="margin: 0;">-<span id="LC4" class="line" lang="markdown">which is available in and GCC >= <span class="idiff left right">4.8 and OSX >= 10.7</span>.</span>

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="markdown">for other operating systems or for development. Mash requires c++1<span class="idiff left right">4</span> to build,</span>

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="markdown">which is available in and GCC >= <span class="idiff left right">5 and XCode >= 6</span>.</span>

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<pre style="margin: 0;"> <span id="LC5" class="line" lang="markdown"></span>

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<pre style="margin: 0;"> <span id="LC6" class="line" lang="markdown">See http://mash.readthedocs.org for more information.</span></pre>

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<li id="10c9d422887ff3796fa73258e801014a688c7a49">

<a href="https://salsa.debian.org/med-team/mash/commit/5e14db80cf1008378399b328c70a9ff7b5c730e4#10c9d422887ff3796fa73258e801014a688c7a49"><strong>doc/sphinx/conf.py</strong></a>

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<pre style="margin: 0;"> <span id="LC43" class="line" lang="python"><span class="n" style="color: #333;">master_doc</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'index'</span></span>

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<pre style="margin: 0;"> <span id="LC44" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC45" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># General information about the project.</span></span>

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<pre style="margin: 0;">-<span id="LC46" class="line" lang="python"><span class="n" style="color: #333;">project</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">u'<span class="idiff left right">m</span>ash'</span></span>

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<pre style="margin: 0;">+<span id="LC46" class="line" lang="python"><span class="n" style="color: #333;">project</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">u'<span class="idiff left right">M</span>ash'</span></span>

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<pre style="margin: 0;"> <span id="LC47" class="line" lang="python"><span class="n" style="color: #333;">copyright</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">u'2015, Brian Ondov, Todd Treangen, Adam Phillippy'</span></span>

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<pre style="margin: 0;"> <span id="LC48" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC49" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># The version info for the project you're documenting, acts as replacement for</span></span>

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<li id="095583c2a50662366c7d4714646e3178e4673738">

<a href="https://salsa.debian.org/med-team/mash/commit/5e14db80cf1008378399b328c70a9ff7b5c730e4#095583c2a50662366c7d4714646e3178e4673738"><strong>doc/sphinx/data.rst</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">@@ -37,24 +37,6 @@ Figure 5:</td>

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<pre style="margin: 0;"> <span id="LC37" class="line" lang="plaintext"> * `fig5.html <https://obj.umiacs.umd.edu/mash/screen/fig5/fig5.html>`_: Interactive version</span>

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<pre style="margin: 0;"> <span id="LC38" class="line" lang="plaintext"> * `fig5.tsv <https://obj.umiacs.umd.edu/mash/screen/fig5/fig5.tsv>`_: Source data</span>

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<pre style="margin: 0;"> <span id="LC39" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">-<span id="LC40" class="line" lang="plaintext">Public data sources</span>

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<pre style="margin: 0;">-<span id="LC41" class="line" lang="plaintext">~~~~~~~~~~~~~~~~~~~</span>

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<pre style="margin: 0;">-<span id="LC42" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">-<span id="LC43" class="line" lang="plaintext">The BLAST ``nr`` database was downloaded from ``ftp://ftp.ncbi.nlm.nih.gov/blast/db/nr.*``.</span>

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<pre style="margin: 0;">-<span id="LC44" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">-<span id="LC45" class="line" lang="plaintext">HMP data were downloaded from ``ftp://public-ftp.ihmpdcc.org/``, reads from the ``Ilumina/`` directory</span>

</pre>

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<pre style="margin: 0;">-<span id="LC46" class="line" lang="plaintext">and coding sequences from the ``HMGI/`` directory. Within these folders, sample SRS015937 resides in</span>

</pre>

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<pre style="margin: 0;">-<span id="LC47" class="line" lang="plaintext">``tongue_dorsum/`` and SRS020263 in ``right_retroauricular_crease/``.</span>

</pre>

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<pre style="margin: 0;">-<span id="LC48" class="line" lang="plaintext"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC49" class="line" lang="plaintext">SRA runs downloaded with the `SRA Toolkit <https://www.ncbi.nlm.nih.gov/sra/docs/toolkitsoft/>`_.</span>

</pre>

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<pre style="margin: 0;">-<span id="LC50" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">-<span id="LC51" class="line" lang="plaintext">RefSeq genomes downloaded from the ``genomes/refseq/`` directory of ``ftp.ncbi.nlm.nih.gov``.</span>

</pre>

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<pre style="margin: 0;">-<span id="LC52" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">-<span id="LC53" class="line" lang="plaintext">Public data products</span>

</pre>

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<pre style="margin: 0;">-<span id="LC54" class="line" lang="plaintext">~~~~~~~~~~~~~~~~~~~~</span>

</pre>

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<pre style="margin: 0;">-<span id="LC55" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">-<span id="LC56" class="line" lang="plaintext">Quebec Polyomavirus is submitted to GenBank as BK010702.</span>

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<pre style="margin: 0;">-<span id="LC57" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC40" class="line" lang="plaintext">Screen of SRA metagenomes vs. RefSeq</span>

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<pre style="margin: 0;"> <span id="LC41" class="line" lang="plaintext">~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~</span>

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<pre style="margin: 0;"> <span id="LC42" 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">@@ -83,3 +65,24 @@ The files are tab separated, with each line beginning with a RefSeq assembly acc</td>

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<pre style="margin: 0;"> <span id="LC65" class="line" lang="plaintext">  GCF_000001215.4    SRR3401361      SRR3540373</span>

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<pre style="margin: 0;"> <span id="LC66" class="line" lang="plaintext">  GCF_000001405.36   SRR5127794      ERR1539652      SRR413753       ERR206081</span>

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<pre style="margin: 0;"> <span id="LC67" class="line" lang="plaintext">  GCF_000001405.38   SRR5127794      ERR1539652      ERR1711677      SRR413753       ERR206081</span>

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<pre style="margin: 0;">+<span id="LC68" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">+<span id="LC69" class="line" lang="plaintext">We also provide simple scripts for searching these files: `search.tar <https://obj.umiacs.umd.edu/mash/screen/search.tar>`_</span>

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<pre style="margin: 0;">+<span id="LC70" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">+<span id="LC71" class="line" lang="plaintext">Public data sources</span>

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<pre style="margin: 0;">+<span id="LC72" class="line" lang="plaintext">~~~~~~~~~~~~~~~~~~~</span>

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<pre style="margin: 0;">+<span id="LC73" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">+<span id="LC74" class="line" lang="plaintext">The BLAST ``nr`` database was downloaded from ``ftp://ftp.ncbi.nlm.nih.gov/blast/db/nr.*``.</span>

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<pre style="margin: 0;">+<span id="LC75" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">+<span id="LC76" class="line" lang="plaintext">HMP data were downloaded from ``ftp://public-ftp.ihmpdcc.org/``, reads from the ``Ilumina/`` directory</span>

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<pre style="margin: 0;">+<span id="LC77" class="line" lang="plaintext">and coding sequences from the ``HMGI/`` directory. Within these folders, sample SRS015937 resides in</span>

</pre>

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<pre style="margin: 0;">+<span id="LC78" class="line" lang="plaintext">``tongue_dorsum/`` and SRS020263 in ``right_retroauricular_crease/``.</span>

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<pre style="margin: 0;">+<span id="LC79" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">+<span id="LC80" class="line" lang="plaintext">SRA runs downloaded with the `SRA Toolkit <https://www.ncbi.nlm.nih.gov/sra/docs/toolkitsoft/>`_.</span>

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<pre style="margin: 0;">+<span id="LC81" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">+<span id="LC82" class="line" lang="plaintext">RefSeq genomes downloaded from the ``genomes/refseq/`` directory of ``ftp.ncbi.nlm.nih.gov``.</span>

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<pre style="margin: 0;">+<span id="LC83" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">+<span id="LC84" class="line" lang="plaintext">Public data products</span>

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<pre style="margin: 0;">+<span id="LC85" class="line" lang="plaintext">~~~~~~~~~~~~~~~~~~~~</span>

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<pre style="margin: 0;">+<span id="LC86" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">+<span id="LC87" class="line" lang="plaintext">Quebec Polyomavirus is submitted to GenBank as BK010702.</span>

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<pre style="margin: 0;">+<span id="LC88" class="line" lang="plaintext"></span></pre>

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<li id="5a765931f4b88491a9e9eb9822872702c171539c">

<a href="https://salsa.debian.org/med-team/mash/commit/5e14db80cf1008378399b328c70a9ff7b5c730e4#5a765931f4b88491a9e9eb9822872702c171539c"><strong>doc/sphinx/index.rst</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">@@ -17,6 +17,8 @@ Publication</td>

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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">===========</span>

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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext">`Mash: fast genome and metagenome distance estimation using MinHash. Ondov BD, Treangen TJ, Melsted P, Mallonee AB, Bergman NH, Koren S, Phillippy AM. Genome Biol. 2016 Jun 20;17(1):132. doi: 10.1186/s13059-016-0997-x. <http://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0997-x>`_</span>

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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">`Mash Screen: High-throughput sequence containment estimation for genome discovery. Ondov BD, Starrett GJ, Sappington A, Kostic A, Koren S, Buck CB, Phillippy AM. BioRxiv. 2019 Mar. doi: 10.1101/557314 <https://doi.org/10.1101/557314>`_</span>

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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext">.. toctree::</span>

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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext">   :maxdepth: 1</span>

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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext">   </span>

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<li id="1b90382419cff5ed5a17e0b2bebbff0c68ecadae">

<a href="https://salsa.debian.org/med-team/mash/commit/5e14db80cf1008378399b328c70a9ff7b5c730e4#1b90382419cff5ed5a17e0b2bebbff0c68ecadae"><strong>src/mash/CommandBounds.cpp</strong></a>

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<pre style="margin: 0;"> <span id="LC85" class="line" lang="cpp">                           </span>

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<pre style="margin: 0;"> <span id="LC86" class="line" lang="cpp">                           <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="n" style="color: #333;">cont</span> <span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC87" class="line" lang="cpp">                           <span class="p">{</span></span>

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<pre style="margin: 0;">-<span id="LC88" class="line" lang="cpp">                                   <span class="n" style="color: #333;">m2j</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">exp</span><span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">dists</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="89" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC88" class="line" lang="cpp">                                   <span class="c1" style="color: #998; font-style: italic;">//m2j = exp(-k * dists[j]);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="89" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC89" class="line" lang="cpp">                                   <span class="n" style="color: #333;">m2j</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pow</span><span class="p">(</span><span class="mf" style="color: #099;">1.0</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">dists</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">],</span> <span class="n" style="color: #333;">k</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// binomial model</span></span>

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<pre style="margin: 0;"> <span id="LC90" class="line" lang="cpp">                           <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC91" class="line" lang="cpp">                           <span class="k" style="font-weight: 600;">else</span></span>

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<pre style="margin: 0;"> <span id="LC92" class="line" lang="cpp">                           <span class="p">{</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="114" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="115" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -114,7 +115,8 @@ int CommandBounds::run() const</td>

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<pre style="margin: 0;"> <span id="LC115" class="line" lang="cpp">                          </span>

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<pre style="margin: 0;"> <span id="LC116" class="line" lang="cpp">                          <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="n" style="color: #333;">cont</span> <span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC117" class="line" lang="cpp">                          <span class="p">{</span></span>

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<pre style="margin: 0;">-<span id="LC117" class="line" lang="cpp">                                  <span class="n" style="color: #333;">j2m</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mf" style="color: #099;">1.0</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">log</span><span class="p">(</span><span class="n" style="color: #333;">je</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC118" class="line" lang="cpp">                                  <span class="c1" style="color: #998; font-style: italic;">//j2m = -1.0 / k * log(je);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC119" class="line" lang="cpp">                                  <span class="n" style="color: #333;">j2m</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">1.0</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">pow</span><span class="p">(</span><span class="n" style="color: #333;">je</span><span class="p">,</span> <span class="mf" style="color: #099;">1.</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">k</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC120" class="line" lang="cpp">                          <span class="p">}</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC121" class="line" lang="cpp">                          <span class="k" style="font-weight: 600;">else</span></span>

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<pre style="margin: 0;"> <span id="LC122" class="line" lang="cpp">                          <span class="p">{</span></span>

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<br>

</li>

<li id="2fffcd35413c3c60b76498e1abc911123672535d">

<a href="https://salsa.debian.org/med-team/mash/commit/5e14db80cf1008378399b328c70a9ff7b5c730e4#2fffcd35413c3c60b76498e1abc911123672535d"><strong>src/mash/CommandDistance.cpp</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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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="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="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -37,6 +37,7 @@ CommandDistance::CommandDistance()</td>

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37

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<pre style="margin: 0;"> <span id="LC37" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">//addOption("log", Option(Option::Boolean, "L", "Output", "Log scale distances and divide by k-mer size to provide a better analog to phylogenetic distance. The special case of zero shared min-hashes will result in a distance of 1.", ""));</span></span>

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<pre style="margin: 0;"> <span id="LC38" class="line" lang="cpp">    <span class="n" style="color: #333;">addOption</span><span class="p">(</span><span class="s" style="color: #d14;">"pvalue"</span><span class="p">,</span> <span class="n" style="color: #333;">Option</span><span class="p">(</span><span class="n" style="color: #333;">Option</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Number</span><span class="p">,</span> <span class="s" style="color: #d14;">"v"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Output"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Maximum p-value to report."</span><span class="p">,</span> <span class="s" style="color: #d14;">"1.0"</span><span class="p">,</span> <span class="mf" style="color: #099;">0.</span><span class="p">,</span> <span class="mf" style="color: #099;">1.</span><span class="p">));</span></span>

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<pre style="margin: 0;"> <span id="LC39" class="line" lang="cpp">    <span class="n" style="color: #333;">addOption</span><span class="p">(</span><span class="s" style="color: #d14;">"distance"</span><span class="p">,</span> <span class="n" style="color: #333;">Option</span><span class="p">(</span><span class="n" style="color: #333;">Option</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Number</span><span class="p">,</span> <span class="s" style="color: #d14;">"d"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Output"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Maximum distance to report."</span><span class="p">,</span> <span class="s" style="color: #d14;">"1.0"</span><span class="p">,</span> <span class="mf" style="color: #099;">0.</span><span class="p">,</span> <span class="mf" style="color: #099;">1.</span><span class="p">));</span></span>

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<pre style="margin: 0;">+<span id="LC40" class="line" lang="cpp">    <span class="n" style="color: #333;">addOption</span><span class="p">(</span><span class="s" style="color: #d14;">"comment"</span><span class="p">,</span> <span class="n" style="color: #333;">Option</span><span class="p">(</span><span class="n" style="color: #333;">Option</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Boolean</span><span class="p">,</span> <span class="s" style="color: #d14;">"C"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Output"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Show comment fields with reference/query names (denoted with ':')."</span><span class="p">,</span> <span class="s" style="color: #d14;">"1.0"</span><span class="p">,</span> <span class="mf" style="color: #099;">0.</span><span class="p">,</span> <span class="mf" style="color: #099;">1.</span><span class="p">));</span></span>

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<pre style="margin: 0;"> <span id="LC41" class="line" lang="cpp">    <span class="n" style="color: #333;">useSketchOptions</span><span class="p">();</span></span>

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<pre style="margin: 0;"> <span id="LC42" class="line" lang="cpp"><span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC43" class="line" lang="cpp"></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="51" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -51,6 +52,7 @@ int CommandDistance::run() const</td>

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<pre style="margin: 0;"> <span id="LC52" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">threads</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">options</span><span class="p">.</span><span class="n" style="color: #333;">at</span><span class="p">(</span><span class="s" style="color: #d14;">"threads"</span><span class="p">).</span><span class="n" style="color: #333;">getArgumentAsNumber</span><span class="p">();</span></span>

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<pre style="margin: 0;"> <span id="LC53" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">list</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">options</span><span class="p">.</span><span class="n" style="color: #333;">at</span><span class="p">(</span><span class="s" style="color: #d14;">"list"</span><span class="p">).</span><span class="n" style="color: #333;">active</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC54" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">table</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">options</span><span class="p">.</span><span class="n" style="color: #333;">at</span><span class="p">(</span><span class="s" style="color: #d14;">"table"</span><span class="p">).</span><span class="n" style="color: #333;">active</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;">bool</span> <span class="n" style="color: #333;">comment</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">options</span><span class="p">.</span><span class="n" style="color: #333;">at</span><span class="p">(</span><span class="s" style="color: #d14;">"comment"</span><span class="p">).</span><span class="n" style="color: #333;">active</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC56" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">//bool log = options.at("log").active;</span></span>

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<pre style="margin: 0;"> <span id="LC57" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">pValueMax</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">options</span><span class="p">.</span><span class="n" style="color: #333;">at</span><span class="p">(</span><span class="s" style="color: #d14;">"pvalue"</span><span class="p">).</span><span class="n" style="color: #333;">getArgumentAsNumber</span><span class="p">();</span></span>

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<pre style="margin: 0;"> <span id="LC58" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">distanceMax</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">options</span><span class="p">.</span><span class="n" style="color: #333;">at</span><span class="p">(</span><span class="s" style="color: #d14;">"distance"</span><span class="p">).</span><span class="n" style="color: #333;">getArgumentAsNumber</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">@@ -225,13 +227,13 @@ int CommandDistance::run() const</td>

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<pre style="margin: 0;"> <span id="LC227" class="line" lang="cpp">        </span>

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<pre style="margin: 0;"> <span id="LC228" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span> <span class="n" style="color: #333;">threadPool</span><span class="p">.</span><span class="n" style="color: #333;">outputAvailable</span><span class="p">()</span> <span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC229" class="line" lang="cpp">        <span class="p">{</span></span>

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<pre style="margin: 0;">-<span id="LC228" class="line" lang="cpp">            <span class="n" style="color: #333;">writeOutput</span><span class="p">(</span><span class="n" style="color: #333;">threadPool</span><span class="p">.</span><span class="n" style="color: #333;">popOutputWhenAvailable</span><span class="p">(),</span> <span class="n" style="color: #333;">table</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC230" class="line" lang="cpp">            <span class="n" style="color: #333;">writeOutput</span><span class="p">(</span><span class="n" style="color: #333;">threadPool</span><span class="p">.</span><span class="n" style="color: #333;">popOutputWhenAvailable</span><span class="p">(),</span> <span class="n" style="color: #333;">table</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">comment</span></span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC231" class="line" lang="cpp">        <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC232" class="line" lang="cpp">    <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC233" class="line" lang="cpp">    </span>

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<pre style="margin: 0;"> <span id="LC234" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span> <span class="n" style="color: #333;">threadPool</span><span class="p">.</span><span class="n" style="color: #333;">running</span><span class="p">()</span> <span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC235" class="line" lang="cpp">    <span class="p">{</span></span>

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<pre style="margin: 0;">-<span id="LC234" class="line" lang="cpp">        <span class="n" style="color: #333;">writeOutput</span><span class="p">(</span><span class="n" style="color: #333;">threadPool</span><span class="p">.</span><span class="n" style="color: #333;">popOutputWhenAvailable</span><span class="p">(),</span> <span class="n" style="color: #333;">table</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC236" class="line" lang="cpp">        <span class="n" style="color: #333;">writeOutput</span><span class="p">(</span><span class="n" style="color: #333;">threadPool</span><span class="p">.</span><span class="n" style="color: #333;">popOutputWhenAvailable</span><span class="p">(),</span> <span class="n" style="color: #333;">table</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">comment</span></span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC237" class="line" lang="cpp">    <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC238" class="line" lang="cpp">    </span>

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<pre style="margin: 0;"> <span id="LC239" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="n" style="color: #333;">warningCount</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span> <span class="n" style="color: #333;">parameters</span><span class="p">.</span><span class="n" style="color: #333;">reads</span> <span class="p">)</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="244" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -242,7 +244,7 @@ int CommandDistance::run() const</td>

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<pre style="margin: 0;"> <span id="LC244" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC245" class="line" lang="cpp"><span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC246" class="line" lang="cpp"></span>

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<pre style="margin: 0;">-<span id="LC245" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">CommandDistance</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">writeOutput</span><span class="p">(</span><span class="n" style="color: #333;">CompareOutput</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">output</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">table</span><span class="p">)</span> <span class="k" style="font-weight: 600;">const</span></span>

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<pre style="margin: 0;">+<span id="LC247" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">CommandDistance</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">writeOutput</span><span class="p">(</span><span class="n" style="color: #333;">CompareOutput</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">output</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">table</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">bool</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">comment</span></span><span class="p">)</span> <span class="k" style="font-weight: 600;">const</span></span>

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<td class="diff-line-num new_line" data-linenumber="248" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC248" class="line" lang="cpp"><span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC249" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">output</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">indexQuery</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC250" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">output</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">indexRef</span><span class="p">;</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="267" style="width: 35px; color: rgba(0,0,0,0.3); 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="269" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -267,7 +269,21 @@ void CommandDistance::writeOutput(CompareOutput * output, bool table) const</td>

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<pre style="margin: 0;"> <span id="LC269" class="line" lang="cpp">        <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC270" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="n" style="color: #333;">pair</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">pass</span> <span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC271" class="line" lang="cpp">        <span class="p">{</span></span>

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<pre style="margin: 0;">-<span id="LC270" class="line" lang="cpp">            <span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">output</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">sketchRef</span><span class="p">.</span><span class="n" style="color: #333;">getReference</span><span class="p">(</span><span class="n" style="color: #333;">j</span><span class="p">).</span><span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;"><<</span> <span class="sc" style="color: #d14;">'\t'</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">output</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">sketchQuery</span><span class="p">.</span><span class="n" style="color: #333;">getReference</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">).</span><span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;"><<</span> <span class="sc" style="color: #d14;">'\t'</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">pair</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">distance</span> <span class="o" style="font-weight: 600;"><<</span> <span class="sc" style="color: #d14;">'\t'</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">pair</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">pValue</span> <span class="o" style="font-weight: 600;"><<</span> <span class="sc" style="color: #d14;">'\t'</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">pair</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">numer</span> <span class="o" style="font-weight: 600;"><<</span> <span class="sc" style="color: #d14;">'/'</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">pair</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">denom</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="LC272" class="line" lang="cpp">            <span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">output</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">sketchRef</span><span class="p">.</span><span class="n" style="color: #333;">getReference</span><span class="p">(</span><span class="n" style="color: #333;">j</span><span class="p">).</span><span class="n" style="color: #333;">name</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC273" class="line" lang="cpp">            </span>

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<pre style="margin: 0;">+<span id="LC274" class="line" lang="cpp">            <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="n" style="color: #333;">comment</span> <span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC275" class="line" lang="cpp">            <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC276" class="line" lang="cpp">                <span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="sc" style="color: #d14;">':'</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">output</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">sketchRef</span><span class="p">.</span><span class="n" style="color: #333;">getReference</span><span class="p">(</span><span class="n" style="color: #333;">j</span><span class="p">).</span><span class="n" style="color: #333;">comment</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC277" class="line" lang="cpp">            <span class="p">}</span></span>

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<pre style="margin: 0;">+<span id="LC278" class="line" lang="cpp">            </span>

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<pre style="margin: 0;">+<span id="LC279" class="line" lang="cpp">            <span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="sc" style="color: #d14;">'\t'</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">output</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">sketchQuery</span><span class="p">.</span><span class="n" style="color: #333;">getReference</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">).</span><span class="n" style="color: #333;">name</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC280" class="line" lang="cpp">            </span>

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<pre style="margin: 0;">+<span id="LC281" class="line" lang="cpp">            <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="n" style="color: #333;">comment</span> <span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC282" class="line" lang="cpp">            <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC283" class="line" lang="cpp">                <span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="sc" style="color: #d14;">':'</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">output</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">sketchQuery</span><span class="p">.</span><span class="n" style="color: #333;">getReference</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">).</span><span class="n" style="color: #333;">comment</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC284" class="line" lang="cpp">            <span class="p">}</span></span>

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<pre style="margin: 0;">+<span id="LC285" class="line" lang="cpp">            </span>

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<pre style="margin: 0;">+<span id="LC286" class="line" lang="cpp">            <span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="sc" style="color: #d14;">'\t'</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">pair</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">distance</span> <span class="o" style="font-weight: 600;"><<</span> <span class="sc" style="color: #d14;">'\t'</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">pair</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">pValue</span> <span class="o" style="font-weight: 600;"><<</span> <span class="sc" style="color: #d14;">'\t'</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">pair</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">numer</span> <span class="o" style="font-weight: 600;"><<</span> <span class="sc" style="color: #d14;">'/'</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">pair</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">denom</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="LC287" class="line" lang="cpp">        <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC288" class="line" lang="cpp">    </span>

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<pre style="margin: 0;"> <span id="LC289" class="line" lang="cpp">        <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>

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<br>

</li>

<li id="d36a6e2bfbbc612f16d6ba17bf5feb1f1e7100e0">

<a href="https://salsa.debian.org/med-team/mash/commit/5e14db80cf1008378399b328c70a9ff7b5c730e4#d36a6e2bfbbc612f16d6ba17bf5feb1f1e7100e0"><strong>src/mash/CommandDistance.h</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="85" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -85,7 +85,7 @@ public:</td>

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<pre style="margin: 0;"> <span id="LC85" class="line" lang="c">    </span>

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<pre style="margin: 0;"> <span id="LC86" class="line" lang="c"><span class="nl">private:</span></span>

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<pre style="margin: 0;"> <span id="LC87" class="line" lang="c">    </span>

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<pre style="margin: 0;">-<span id="LC88" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">writeOutput</span><span class="p">(</span><span class="n" style="color: #333;">CompareOutput</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">output</span><span class="p">,</span> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">table</span><span class="p">)</span> <span class="k" style="font-weight: 600;">const</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC88" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">writeOutput</span><span class="p">(</span><span class="n" style="color: #333;">CompareOutput</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">output</span><span class="p">,</span> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">table</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">bool</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">comment</span></span><span class="p">)</span> <span class="k" style="font-weight: 600;">const</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC89" class="line" lang="c"><span class="p">};</span></span>

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<pre style="margin: 0;"> <span id="LC90" class="line" lang="c"></span>

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<pre style="margin: 0;"> <span id="LC91" class="line" lang="c"><span class="n" style="color: #333;">CommandDistance</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">CompareOutput</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">compare</span><span class="p">(</span><span class="n" style="color: #333;">CommandDistance</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">CompareInput</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">input</span><span class="p">);</span></span>

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<br>

</li>

<li id="b1869287016c57e645de15f0b9ede057292d44b7">

<a href="https://salsa.debian.org/med-team/mash/commit/5e14db80cf1008378399b328c70a9ff7b5c730e4#b1869287016c57e645de15f0b9ede057292d44b7"><strong>src/mash/CommandScreen.cpp</strong></a>

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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -39,9 +39,9 @@ CommandScreen::CommandScreen()</td>

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<pre style="margin: 0;"> <span id="LC39" class="line" lang="cpp"><span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">Command</span><span class="p">()</span></span>

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<pre style="margin: 0;"> <span id="LC40" class="line" lang="cpp"><span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC41" class="line" lang="cpp">   <span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"screen"</span><span class="p">;</span></span>

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<pre style="margin: 0;">-<span id="LC42" class="line" lang="cpp">   <span class="n" style="color: #333;">summary</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"Determine whether query sequences are within a larger <span class="idiff left right">pool</span> of sequences."</span><span class="p">;</span></span>

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<pre style="margin: 0;">-<span id="LC43" class="line" lang="cpp">   <span class="n" style="color: #333;">description</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"Determine how well query sequences are contained within a <span class="idiff left">pool of sequences. The queries must be formatted as a single Mash sketch file (.msh), created with the `mash sketch` command. The <pool> files can be contigs or reads, in fasta or fastq, gzipped or not, and </span></span><span class="se" style="color: #d14;"><span class="idiff">\"</span></span><span class="s" style="color: #d14;"><span class="idiff">-</span></span><span class="se" style="color: #d14;"><span class="idiff">\"</span></span><span class="s" style="color: #d14;"><span class="idiff right"> can be given for <pool> to read from standard input. The <pool> sequences are assumed to be nucleotides, and will be 6-frame translated if the <queries> are amino acids. The output fields are [identity, shared-hashes, median-multiplicity, p-value, query-ID, query-comment], where median-multiplicity is computed for shared hashes, based on the number of observations of those hashes within the pool</span>."</span><span class="p">;</span></span>

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<pre style="margin: 0;">-<span id="LC44" class="line" lang="cpp">    <span class="n" style="color: #333;">argumentString</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"<queries>.msh <<span class="idiff left right">pool> [<pool</span>>] ..."</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC42" class="line" lang="cpp">   <span class="n" style="color: #333;">summary</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"Determine whether query sequences are within a larger <span class="idiff left right">mixture</span> of sequences."</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC43" class="line" lang="cpp">   <span class="n" style="color: #333;">description</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"Determine how well query sequences are contained within a <span class="idiff left">mixture of sequences. The queries must be formatted as a single Mash sketch file (.msh), created with the `mash sketch` command. The <mixture> files can be contigs or reads, in fasta or fastq, gzipped or not, and </span></span><span class="se" style="color: #d14;"><span class="idiff">\"</span></span><span class="s" style="color: #d14;"><span class="idiff">-</span></span><span class="se" style="color: #d14;"><span class="idiff">\"</span></span><span class="s" style="color: #d14;"><span class="idiff right"> can be given for <mixture> to read from standard input. The <mixture> sequences are assumed to be nucleotides, and will be 6-frame translated if the <queries> are amino acids. The output fields are [identity, shared-hashes, median-multiplicity, p-value, query-ID, query-comment], where median-multiplicity is computed for shared hashes, based on the number of observations of those hashes within the mixture</span>."</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC44" class="line" lang="cpp">    <span class="n" style="color: #333;">argumentString</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"<queries>.msh <<span class="idiff left right">mixture> [<mixture</span>>] ..."</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC45" class="line" lang="cpp">   </span>

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<pre style="margin: 0;"> <span id="LC46" class="line" lang="cpp">   <span class="n" style="color: #333;">useOption</span><span class="p">(</span><span class="s" style="color: #d14;">"help"</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;">useOption</span><span class="p">(</span><span class="s" style="color: #d14;">"threads"</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">@@ -322,7 +322,7 @@ int CommandScreen::run() const</td>

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<pre style="margin: 0;"> <span id="LC322" 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="LC323" class="line" lang="cpp">  </span>

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<pre style="margin: 0;"> <span id="LC324" class="line" lang="cpp">  <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">setSize</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">minHashHeap</span><span class="p">.</span><span class="n" style="color: #333;">estimateSetSize</span><span class="p">();</span></span>

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325

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<pre style="margin: 0;">-<span id="LC325" 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;">"   Estimated distinct"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="p">(</span><span class="n" style="color: #333;">trans</span> <span class="o" style="font-weight: 600;">?</span> <span class="s" style="color: #d14;">" (translated)"</span> <span class="o" style="font-weight: 600;">:</span> <span class="s" style="color: #d14;">""</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" k-mers in <span class="idiff left right">pool</span>: "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">setSize</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

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<td class="diff-line-num new old_line" data-linenumber="326" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC325" 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;">"   Estimated distinct"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="p">(</span><span class="n" style="color: #333;">trans</span> <span class="o" style="font-weight: 600;">?</span> <span class="s" style="color: #d14;">" (translated)"</span> <span class="o" style="font-weight: 600;">:</span> <span class="s" style="color: #d14;">""</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" k-mers in <span class="idiff left right">mixture</span>: "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">setSize</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="LC326" class="line" lang="cpp">  </span>

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<pre style="margin: 0;"> <span id="LC327" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="n" style="color: #333;">setSize</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="LC328" class="line" lang="cpp">  <span class="p">{</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="606" style="width: 35px; color: rgba(0,0,0,0.3); 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="606" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -606,7 +606,7 @@ double pValueWithin(uint64_t x, uint64_t setSize, double kmerSpace, uint64_t ske</td>

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<pre style="margin: 0;"> <span id="LC606" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">return</span> <span class="mf" style="color: #099;">1.</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC607" class="line" lang="cpp">    <span class="p">}</span></span>

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<td class="diff-line-num old_line" data-linenumber="608" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="608" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

608

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<pre style="margin: 0;"> <span id="LC608" class="line" lang="cpp">    </span>

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<td class="diff-line-num old old_line" data-linenumber="609" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="609" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC609" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">r</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;"><span class="idiff left">1.</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">/</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="mf" style="color: #099;"><span class="idiff">1.</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">kmerSpace</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">setSize</span></span><span class="p"><span class="idiff right">)</span>;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="610" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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609

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<pre style="margin: 0;">+<span id="LC609" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">r</span> <span class="o" style="font-weight: 600;">=</span> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">double</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">setSize</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">/</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">kmerSpace</span></span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="610" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

610

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<td class="diff-line-num new_line" data-linenumber="610" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

610

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<pre style="margin: 0;"> <span id="LC610" class="line" lang="cpp">    </span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="611" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

611

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611

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<pre style="margin: 0;"> <span id="LC611" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#ifdef USE_BOOST</span></span>

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<td class="diff-line-num old_line" data-linenumber="612" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

612

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<td class="diff-line-num new_line" data-linenumber="612" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

612

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<pre style="margin: 0;"> <span id="LC612" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">cdf</span><span class="p">(</span><span class="n" style="color: #333;">complement</span><span class="p">(</span><span class="n" style="color: #333;">binomial</span><span class="p">(</span><span class="n" style="color: #333;">sketchSize</span><span class="p">,</span> <span class="n" style="color: #333;">r</span><span class="p">),</span> <span class="n" style="color: #333;">x</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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<li id="c1907300070128758e5df535932ad22cf1b51bf9">

<a href="https://salsa.debian.org/med-team/mash/commit/5e14db80cf1008378399b328c70a9ff7b5c730e4#c1907300070128758e5df535932ad22cf1b51bf9"><strong>src/mash/CommandScreen.h</strong></a>

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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="n" style="color: #333;">namespace</span> <span class="n" style="color: #333;">mash</span> <span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC21" class="line" lang="c"></span>

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<td class="diff-line-num new old_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC22" class="line" lang="c"><span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">HashTableEntry</span></span>

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<pre style="margin: 0;">+<span id="LC23" class="line" lang="c"><span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC24" class="line" lang="c">     <span class="n" style="color: #333;">HashTableEntry</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;">0</span><span class="p">)</span> <span class="p">{}</span></span>

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<pre style="margin: 0;">+<span id="LC25" class="line" lang="c">     </span>

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<pre style="margin: 0;">+<span id="LC26" class="line" lang="c">     <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">count</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC27" class="line" lang="c">     <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">unordered_set</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">uint64_t</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">indices</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC28" class="line" lang="c"><span class="p">};</span></span>

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<pre style="margin: 0;">+<span id="LC29" class="line" lang="c"></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;">//typedef std::unordered_map< uint64_t, HashTableEntry > HashTable;</span></span>

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<pre style="margin: 0;"> <span id="LC31" class="line" lang="c"><span class="k" style="font-weight: 600;">typedef</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">unordered_map</span><span class="o" style="font-weight: 600;"><</span> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</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;">unordered_set</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">uint64_t</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">HashTable</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC32" class="line" lang="c"></span>

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<pre style="margin: 0;"> <span id="LC33" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">unordered_map</span><span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">codons</span> <span class="o" style="font-weight: 600;">=</span></span>

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</li>

<li id="e8b45cfb4cd2406e50d5c27273b019116a793f02">

<a href="https://salsa.debian.org/med-team/mash/commit/5e14db80cf1008378399b328c70a9ff7b5c730e4#e8b45cfb4cd2406e50d5c27273b019116a793f02"><strong>src/mash/CommandTriangle.cpp</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="35" style="width: 35px; color: rgba(0,0,0,0.3); 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="35" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -35,6 +35,9 @@ CommandTriangle::CommandTriangle()</td>

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<pre style="margin: 0;"> <span id="LC35" class="line" lang="cpp">    <span class="n" style="color: #333;">useOption</span><span class="p">(</span><span class="s" style="color: #d14;">"help"</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC36" class="line" lang="cpp">    <span class="n" style="color: #333;">addOption</span><span class="p">(</span><span class="s" style="color: #d14;">"list"</span><span class="p">,</span> <span class="n" style="color: #333;">Option</span><span class="p">(</span><span class="n" style="color: #333;">Option</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Boolean</span><span class="p">,</span> <span class="s" style="color: #d14;">"l"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Input"</span><span class="p">,</span> <span class="s" style="color: #d14;">"List input. Lines in each <query> specify paths to sequence files, one per line. The reference file is not affected."</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">));</span></span>

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<pre style="margin: 0;"> <span id="LC37" class="line" lang="cpp">    <span class="n" style="color: #333;">addOption</span><span class="p">(</span><span class="s" style="color: #d14;">"comment"</span><span class="p">,</span> <span class="n" style="color: #333;">Option</span><span class="p">(</span><span class="n" style="color: #333;">Option</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Boolean</span><span class="p">,</span> <span class="s" style="color: #d14;">"C"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Output"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Use comment fields for sequence names instead of IDs."</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">));</span></span>

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<pre style="margin: 0;">+<span id="LC38" class="line" lang="cpp">    <span class="n" style="color: #333;">addOption</span><span class="p">(</span><span class="s" style="color: #d14;">"edge"</span><span class="p">,</span> <span class="n" style="color: #333;">Option</span><span class="p">(</span><span class="n" style="color: #333;">Option</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Boolean</span><span class="p">,</span> <span class="s" style="color: #d14;">"E"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Output"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Output edge list instead of Phylip matrix, with fields [seq1, seq2, dist, p-val, shared-hashes]."</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">));</span></span>

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<pre style="margin: 0;">+<span id="LC39" class="line" lang="cpp">    <span class="n" style="color: #333;">addOption</span><span class="p">(</span><span class="s" style="color: #d14;">"pvalue"</span><span class="p">,</span> <span class="n" style="color: #333;">Option</span><span class="p">(</span><span class="n" style="color: #333;">Option</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Number</span><span class="p">,</span> <span class="s" style="color: #d14;">"v"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Output"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Maximum p-value to report in edge list. Implies -"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">getOption</span><span class="p">(</span><span class="s" style="color: #d14;">"edge"</span><span class="p">).</span><span class="n" style="color: #333;">identifier</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"."</span><span class="p">,</span> <span class="s" style="color: #d14;">"1.0"</span><span class="p">,</span> <span class="mf" style="color: #099;">0.</span><span class="p">,</span> <span class="mf" style="color: #099;">1.</span><span class="p">));</span></span>

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<pre style="margin: 0;">+<span id="LC40" class="line" lang="cpp">    <span class="n" style="color: #333;">addOption</span><span class="p">(</span><span class="s" style="color: #d14;">"distance"</span><span class="p">,</span> <span class="n" style="color: #333;">Option</span><span class="p">(</span><span class="n" style="color: #333;">Option</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Number</span><span class="p">,</span> <span class="s" style="color: #d14;">"d"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Output"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Maximum distance to report in edge list. Implies -"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">getOption</span><span class="p">(</span><span class="s" style="color: #d14;">"edge"</span><span class="p">).</span><span class="n" style="color: #333;">identifier</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"."</span><span class="p">,</span> <span class="s" style="color: #d14;">"1.0"</span><span class="p">,</span> <span class="mf" style="color: #099;">0.</span><span class="p">,</span> <span class="mf" style="color: #099;">1.</span><span class="p">));</span></span>

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<pre style="margin: 0;"> <span id="LC41" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">//addOption("log", Option(Option::Boolean, "L", "Output", "Log scale distances and divide by k-mer size to provide a better analog to phylogenetic distance. The special case of zero shared min-hashes will result in a distance of 1.", ""));</span></span>

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<pre style="margin: 0;"> <span id="LC42" class="line" lang="cpp">    <span class="n" style="color: #333;">useSketchOptions</span><span class="p">();</span></span>

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<pre style="margin: 0;"> <span id="LC43" class="line" lang="cpp"><span class="p">}</span></span>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -50,8 +53,16 @@ int CommandTriangle::run() const</td>

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<pre style="margin: 0;"> <span id="LC53" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">threads</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">options</span><span class="p">.</span><span class="n" style="color: #333;">at</span><span class="p">(</span><span class="s" style="color: #d14;">"threads"</span><span class="p">).</span><span class="n" style="color: #333;">getArgumentAsNumber</span><span class="p">();</span></span>

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<pre style="margin: 0;"> <span id="LC54" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">list</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">options</span><span class="p">.</span><span class="n" style="color: #333;">at</span><span class="p">(</span><span class="s" style="color: #d14;">"list"</span><span class="p">).</span><span class="n" style="color: #333;">active</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC55" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">//bool log = options.at("log").active;</span></span>

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<pre style="margin: 0;">-<span id="LC53" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">pValueMax</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="LC56" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">comment</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">options</span><span class="p">.</span><span class="n" style="color: #333;">at</span><span class="p">(</span><span class="s" style="color: #d14;">"comment"</span><span class="p">).</span><span class="n" style="color: #333;">active</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC57" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">edge</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">options</span><span class="p">.</span><span class="n" style="color: #333;">at</span><span class="p">(</span><span class="s" style="color: #d14;">"edge"</span><span class="p">).</span><span class="n" style="color: #333;">active</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC58" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">pValueMax</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">options</span><span class="p">.</span><span class="n" style="color: #333;">at</span><span class="p">(</span><span class="s" style="color: #d14;">"pvalue"</span><span class="p">).</span><span class="n" style="color: #333;">getArgumentAsNumber</span><span class="p">();</span></span>

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<td class="diff-line-num new new_line" data-linenumber="59" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC59" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">distanceMax</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">options</span><span class="p">.</span><span class="n" style="color: #333;">at</span><span class="p">(</span><span class="s" style="color: #d14;">"distance"</span><span class="p">).</span><span class="n" style="color: #333;">getArgumentAsNumber</span><span class="p">();</span></span>

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<pre style="margin: 0;">+<span id="LC60" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">pValuePeakToSet</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC61" class="line" lang="cpp">    </span>

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<pre style="margin: 0;">+<span id="LC62" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="n" style="color: #333;">options</span><span class="p">.</span><span class="n" style="color: #333;">at</span><span class="p">(</span><span class="s" style="color: #d14;">"pvalue"</span><span class="p">).</span><span class="n" style="color: #333;">active</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">options</span><span class="p">.</span><span class="n" style="color: #333;">at</span><span class="p">(</span><span class="s" style="color: #d14;">"distance"</span><span class="p">).</span><span class="n" style="color: #333;">active</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>

</pre>

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<pre style="margin: 0;">+<span id="LC64" class="line" lang="cpp">        <span class="n" style="color: #333;">edge</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC65" class="line" lang="cpp">    <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC66" class="line" lang="cpp">    </span>

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<pre style="margin: 0;"> <span id="LC67" class="line" lang="cpp">    <span class="n" style="color: #333;">Sketch</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Parameters</span> <span class="n" style="color: #333;">parameters</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC68" class="line" lang="cpp">    </span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="120" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -109,27 +120,33 @@ int CommandTriangle::run() const</td>

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<pre style="margin: 0;"> <span id="LC120" class="line" lang="cpp">          <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC121" class="line" lang="cpp">  <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC122" class="line" lang="cpp">    </span>

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<pre style="margin: 0;">-<span id="LC112" class="line" lang="cpp">    <span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="sc" style="color: #d14;">'\t'</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">sketch</span><span class="p">.</span><span class="n" style="color: #333;">getReferenceCount</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

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<pre style="margin: 0;">-<span id="LC113" class="line" lang="cpp">    <span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="p">(</span><span class="n" style="color: #333;">comment</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">sketch</span><span class="p">.</span><span class="n" style="color: #333;">getReference</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">).</span><span class="n" style="color: #333;">comment</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">sketch</span><span class="p">.</span><span class="n" style="color: #333;">getReference</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">).</span><span class="n" style="color: #333;">name</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

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<td class="diff-line-num new old_line" data-linenumber="114" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="123" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

123

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC123" 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;">edge</span> <span class="p">)</span></span>

</pre>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="114" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="124" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

124

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC124" class="line" lang="cpp">    <span class="p">{</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="114" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="125" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

125

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC125" class="line" lang="cpp">        <span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="sc" style="color: #d14;">'\t'</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">sketch</span><span class="p">.</span><span class="n" style="color: #333;">getReferenceCount</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="114" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

126

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<pre style="margin: 0;">+<span id="LC126" class="line" lang="cpp">        <span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="p">(</span><span class="n" style="color: #333;">comment</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">sketch</span><span class="p">.</span><span class="n" style="color: #333;">getReference</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">).</span><span class="n" style="color: #333;">comment</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">sketch</span><span class="p">.</span><span class="n" style="color: #333;">getReference</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">).</span><span class="n" style="color: #333;">name</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="114" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

127

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<pre style="margin: 0;">+<span id="LC127" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="114" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

114

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<td class="diff-line-num new_line" data-linenumber="128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

128

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC128" class="line" lang="cpp">    </span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="115" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

115

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<td class="diff-line-num new_line" data-linenumber="129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

129

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<pre style="margin: 0;"> <span id="LC129" class="line" lang="cpp">    <span class="n" style="color: #333;">ThreadPool</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">TriangleInput</span><span class="p">,</span> <span class="n" style="color: #333;">TriangleOutput</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">threadPool</span><span class="p">(</span><span class="n" style="color: #333;">compare</span><span class="p">,</span> <span class="n" style="color: #333;">threads</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="116" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

116

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<td class="diff-line-num new_line" data-linenumber="130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

130

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<pre style="margin: 0;"> <span id="LC130" class="line" lang="cpp">    </span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="117" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

117

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<td class="diff-line-num new_line" data-linenumber="131" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

131

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<pre style="margin: 0;"> <span id="LC131" 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;">uint64_t</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;">sketch</span><span class="p">.</span><span class="n" style="color: #333;">getReferenceCount</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>

</pre>

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<td class="diff-line-num old_line" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

118

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<td class="diff-line-num new_line" data-linenumber="132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

132

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<pre style="margin: 0;"> <span id="LC132" class="line" lang="cpp">    <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

119

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<td class="diff-line-num new_line old" data-linenumber="133" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC119" class="line" lang="cpp">        <span class="n" style="color: #333;">threadPool</span><span class="p">.</span><span class="n" style="color: #333;">runWhenThreadAvailable</span><span class="p">(</span><span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">TriangleInput</span><span class="p">(</span><span class="n" style="color: #333;">sketch</span><span class="p">,</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">parameters</span><span class="p">));</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="120" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="133" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC133" class="line" lang="cpp">        <span class="n" style="color: #333;">threadPool</span><span class="p">.</span><span class="n" style="color: #333;">runWhenThreadAvailable</span><span class="p">(</span><span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">TriangleInput</span><span class="p">(</span><span class="n" style="color: #333;">sketch</span><span class="p">,</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">parameters</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">distanceMax</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">pValueMax</span></span><span class="p">));</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="120" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

120

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<td class="diff-line-num new_line" data-linenumber="134" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

134

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<pre style="margin: 0;"> <span id="LC134" class="line" lang="cpp">        </span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="121" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

121

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<td class="diff-line-num new_line" data-linenumber="135" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

135

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<pre style="margin: 0;"> <span id="LC135" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span> <span class="n" style="color: #333;">threadPool</span><span class="p">.</span><span class="n" style="color: #333;">outputAvailable</span><span class="p">()</span> <span class="p">)</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="122" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

122

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<td class="diff-line-num new_line" data-linenumber="136" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

136

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC136" class="line" lang="cpp">        <span class="p">{</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="123" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

123

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<td class="diff-line-num new_line old" data-linenumber="137" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC123" class="line" lang="cpp">            <span class="n" style="color: #333;">writeOutput</span><span class="p">(</span><span class="n" style="color: #333;">threadPool</span><span class="p">.</span><span class="n" style="color: #333;">popOutputWhenAvailable</span><span class="p">(),</span> <span class="n" style="color: #333;">comment</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">pValueMax</span></span><span class="p">);</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="124" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="137" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC137" class="line" lang="cpp">            <span class="n" style="color: #333;">writeOutput</span><span class="p">(</span><span class="n" style="color: #333;">threadPool</span><span class="p">.</span><span class="n" style="color: #333;">popOutputWhenAvailable</span><span class="p">(),</span> <span class="n" style="color: #333;">comment</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">edge</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">pValuePeakToSet</span></span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="124" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

124

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<td class="diff-line-num new_line" data-linenumber="138" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

138

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<pre style="margin: 0;"> <span id="LC138" class="line" lang="cpp">        <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="125" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

125

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<td class="diff-line-num new_line" data-linenumber="139" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

139

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<pre style="margin: 0;"> <span id="LC139" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

126

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<td class="diff-line-num new_line" data-linenumber="140" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

140

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<pre style="margin: 0;"> <span id="LC140" class="line" lang="cpp">    </span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

127

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<td class="diff-line-num new_line" data-linenumber="141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

141

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<pre style="margin: 0;"> <span id="LC141" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span> <span class="n" style="color: #333;">threadPool</span><span class="p">.</span><span class="n" style="color: #333;">running</span><span class="p">()</span> <span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

128

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<td class="diff-line-num new_line" data-linenumber="142" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

142

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<pre style="margin: 0;"> <span id="LC142" class="line" lang="cpp">    <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

129

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<td class="diff-line-num new_line old" data-linenumber="143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC129" class="line" lang="cpp">        <span class="n" style="color: #333;">writeOutput</span><span class="p">(</span><span class="n" style="color: #333;">threadPool</span><span class="p">.</span><span class="n" style="color: #333;">popOutputWhenAvailable</span><span class="p">(),</span> <span class="n" style="color: #333;">comment</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">pValueMax</span></span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC143" class="line" lang="cpp">        <span class="n" style="color: #333;">writeOutput</span><span class="p">(</span><span class="n" style="color: #333;">threadPool</span><span class="p">.</span><span class="n" style="color: #333;">popOutputWhenAvailable</span><span class="p">(),</span> <span class="n" style="color: #333;">comment</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">edge</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">pValuePeakToSet</span></span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="144" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC144" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="131" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="145" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

145

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<pre style="margin: 0;"> <span id="LC145" class="line" lang="cpp">    </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="146" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC132" 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;">"Max p-value: "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">pValueMax</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="133" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="146" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC146" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">edge</span> <span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="133" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="147" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC147" class="line" lang="cpp">    <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="133" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC148" 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;">"Max p-value: "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">pValuePeakToSet</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="133" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC149" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="133" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="150" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

150

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC150" class="line" lang="cpp">    </span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="134" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="151" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

151

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC151" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="n" style="color: #333;">warningCount</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span> <span class="n" style="color: #333;">parameters</span><span class="p">.</span><span class="n" style="color: #333;">reads</span> <span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="135" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

135

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<td class="diff-line-num new_line" data-linenumber="152" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

152

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC152" class="line" lang="cpp">    <span class="p">{</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="139" style="width: 35px; color: rgba(0,0,0,0.3); 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="156" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -139,23 +156,43 @@ int CommandTriangle::run() const</td>

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<td class="diff-line-num old_line" data-linenumber="139" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

139

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<td class="diff-line-num new_line" data-linenumber="156" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

156

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<pre style="margin: 0;"> <span id="LC156" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="140" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

140

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<td class="diff-line-num new_line" data-linenumber="157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

157

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<pre style="margin: 0;"> <span id="LC157" class="line" lang="cpp"><span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

141

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<td class="diff-line-num new_line" data-linenumber="158" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

158

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC158" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="142" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

142

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<td class="diff-line-num new_line old" data-linenumber="159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC142" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">CommandTriangle</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">writeOutput</span><span class="p">(</span><span class="n" style="color: #333;">TriangleOutput</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">output</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">comment</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">double</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">pValueMax</span></span><span class="p">)</span> <span class="k" style="font-weight: 600;">const</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

159

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<pre style="margin: 0;">+<span id="LC159" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">CommandTriangle</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">writeOutput</span><span class="p">(</span><span class="n" style="color: #333;">TriangleOutput</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">output</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">comment</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">bool</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">edge</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">double</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">pValuePeakToSet</span></span><span class="p">)</span> <span class="k" style="font-weight: 600;">const</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

143

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<td class="diff-line-num new_line" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

160

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<pre style="margin: 0;"> <span id="LC160" class="line" lang="cpp"><span class="p">{</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="144" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC144" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Sketch</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">sketch</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">output</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">sketch</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="145" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

145

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<td class="diff-line-num new_line old" data-linenumber="161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC145" class="line" lang="cpp">  <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Sketch</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Reference</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">ref</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sketch</span><span class="p">.</span><span class="n" style="color: #333;">getReference</span><span class="p">(</span><span class="n" style="color: #333;">output</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">index</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="146" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

146

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<td class="diff-line-num new_line old" data-linenumber="161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC146" class="line" lang="cpp">  </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="147" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC147" class="line" lang="cpp">  <span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="p">(</span><span class="n" style="color: #333;">comment</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">ref</span><span class="p">.</span><span class="n" style="color: #333;">comment</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">ref</span><span class="p">.</span><span class="n" style="color: #333;">name</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC148" class="line" lang="cpp">  </span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

161

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<pre style="margin: 0;">+<span id="LC161" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Sketch</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">sketch</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">output</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">sketch</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC162" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Sketch</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Reference</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">ref</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sketch</span><span class="p">.</span><span class="n" style="color: #333;">getReference</span><span class="p">(</span><span class="n" style="color: #333;">output</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">index</span><span class="p">);</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="163" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

163

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<pre style="margin: 0;">+<span id="LC163" class="line" lang="cpp">    </span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="164" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC164" 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;">edge</span> <span class="p">)</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="165" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC165" class="line" lang="cpp">    <span class="p">{</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="166" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC166" class="line" lang="cpp">        <span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="p">(</span><span class="n" style="color: #333;">comment</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">ref</span><span class="p">.</span><span class="n" style="color: #333;">comment</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">ref</span><span class="p">.</span><span class="n" style="color: #333;">name</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="167" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

167

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<pre style="margin: 0;">+<span id="LC167" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="168" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

168

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<pre style="margin: 0;">+<span id="LC168" class="line" lang="cpp">    </span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

149

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<td class="diff-line-num new_line" data-linenumber="169" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

169

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<pre style="margin: 0;"> <span id="LC169" 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;">uint64_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;">output</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">index</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span> <span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="150" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

150

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<td class="diff-line-num new_line" data-linenumber="170" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

170

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<pre style="margin: 0;"> <span id="LC170" class="line" lang="cpp">    <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="151" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

151

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<td class="diff-line-num new_line" data-linenumber="171" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

171

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<pre style="margin: 0;"> <span id="LC171" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">CommandDistance</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">CompareOutput</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">PairOutput</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">pair</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">output</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">pairs</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="152" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

152

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<td class="diff-line-num new_line old" data-linenumber="172" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC152" class="line" lang="cpp">      <span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="sc" style="color: #d14;">'\t'</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">pair</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">distance</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="153" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

153

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<td class="diff-line-num new_line old" data-linenumber="172" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC153" class="line" lang="cpp">      <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="n" style="color: #333;">pair</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">pValue</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">pValueMax</span> <span class="p">)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="154" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

154

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<td class="diff-line-num new_line old" data-linenumber="172" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC154" class="line" lang="cpp">      <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="155" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

155

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<td class="diff-line-num new_line old" data-linenumber="172" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC155" class="line" lang="cpp">          <span class="n" style="color: #333;">pValueMax</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pair</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">pValue</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="156" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

156

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<td class="diff-line-num new_line old" data-linenumber="172" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC156" class="line" lang="cpp">      <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="172" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC172" class="line" lang="cpp">        </span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="173" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

173

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<pre style="margin: 0;">+<span id="LC173" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="n" style="color: #333;">edge</span> <span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="174" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

174

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<pre style="margin: 0;">+<span id="LC174" class="line" lang="cpp">        <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="175" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC175" class="line" lang="cpp">            <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="n" style="color: #333;">pair</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">pass</span> <span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="176" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

176

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<pre style="margin: 0;">+<span id="LC176" class="line" lang="cpp">            <span class="p">{</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="177" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC177" class="line" lang="cpp">                <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Sketch</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Reference</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">qry</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sketch</span><span class="p">.</span><span class="n" style="color: #333;">getReference</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="178" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC178" class="line" lang="cpp">                <span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="p">(</span><span class="n" style="color: #333;">comment</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">ref</span><span class="p">.</span><span class="n" style="color: #333;">comment</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">ref</span><span class="p">.</span><span class="n" style="color: #333;">name</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><<</span> <span class="sc" style="color: #d14;">'\t'</span><span class="o" style="font-weight: 600;"><<</span> <span class="p">(</span><span class="n" style="color: #333;">comment</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">qry</span><span class="p">.</span><span class="n" style="color: #333;">comment</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">qry</span><span class="p">.</span><span class="n" style="color: #333;">name</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><<</span> <span class="sc" style="color: #d14;">'\t'</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">pair</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">distance</span> <span class="o" style="font-weight: 600;"><<</span> <span class="sc" style="color: #d14;">'\t'</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">pair</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">pValue</span> <span class="o" style="font-weight: 600;"><<</span> <span class="sc" style="color: #d14;">'\t'</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">pair</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">numer</span> <span class="o" style="font-weight: 600;"><<</span> <span class="sc" style="color: #d14;">'/'</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">pair</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">denom</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="179" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

179

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<pre style="margin: 0;">+<span id="LC179" class="line" lang="cpp">            <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="180" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

180

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<pre style="margin: 0;">+<span id="LC180" class="line" lang="cpp">        <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="181" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

181

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<pre style="margin: 0;">+<span id="LC181" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">else</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="182" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

182

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<pre style="margin: 0;">+<span id="LC182" class="line" lang="cpp">        <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="183" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

183

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<pre style="margin: 0;">+<span id="LC183" class="line" lang="cpp">            <span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="sc" style="color: #d14;">'\t'</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">pair</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">distance</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="184" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

184

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<pre style="margin: 0;">+<span id="LC184" class="line" lang="cpp">        <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="185" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

185

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<pre style="margin: 0;">+<span id="LC185" class="line" lang="cpp">        </span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="186" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

186

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<pre style="margin: 0;">+<span id="LC186" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span> <span class="n" style="color: #333;">pair</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">pValue</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">pValuePeakToSet</span> <span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="187" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

187

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<pre style="margin: 0;">+<span id="LC187" class="line" lang="cpp">        <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="188" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

188

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<pre style="margin: 0;">+<span id="LC188" class="line" lang="cpp">            <span class="n" style="color: #333;">pValuePeakToSet</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pair</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">pValue</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="189" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

189

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<pre style="margin: 0;">+<span id="LC189" class="line" lang="cpp">        <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="190" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

190

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<pre style="margin: 0;">+<span id="LC190" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="191" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

191

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<pre style="margin: 0;">+<span id="LC191" class="line" lang="cpp">    </span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="192" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

192

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<pre style="margin: 0;">+<span id="LC192" 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;">edge</span> <span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

193

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<pre style="margin: 0;">+<span id="LC193" class="line" lang="cpp">    <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="194" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

194

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<pre style="margin: 0;">+<span id="LC194" class="line" lang="cpp">        <span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

</pre>

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157

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<td class="diff-line-num new_line" data-linenumber="195" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

195

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<pre style="margin: 0;"> <span id="LC195" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="158" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC158" class="line" lang="cpp">  <span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>

</pre>

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159

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196

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<pre style="margin: 0;"> <span id="LC196" class="line" lang="cpp">    </span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

160

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197

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<pre style="margin: 0;"> <span id="LC197" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">delete</span> <span class="n" style="color: #333;">output</span><span class="p">;</span></span>

</pre>

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198

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<pre style="margin: 0;"> <span id="LC198" class="line" lang="cpp"><span class="p">}</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="170" style="width: 35px; color: rgba(0,0,0,0.3); 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="207" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -170,7 +207,7 @@ CommandTriangle::TriangleOutput * compare(CommandTriangle::TriangleInput * input</td>

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<pre style="margin: 0;"> <span id="LC207" class="line" lang="cpp">    </span>

</pre>

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<pre style="margin: 0;"> <span id="LC208" 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;">uint64_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;">input</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">index</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span> <span class="p">)</span></span>

</pre>

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172

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209

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<pre style="margin: 0;"> <span id="LC209" class="line" lang="cpp">    <span class="p">{</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC173" class="line" lang="cpp">    <span class="idiff left">     </span><span class="n" style="color: #333;"><span class="idiff">compareSketches</span></span><span class="p"><span class="idiff">(</span></span><span class="o" style="font-weight: 600;"><span class="idiff">&</span></span><span class="n" style="color: #333;"><span class="idiff">output</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">pairs</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="p"><span class="idiff">],</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">sketch</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">getReference</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">input</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">index</span></span><span class="p"><span class="idiff">),</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">sketch</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">getReference</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="p"><span class="idiff">),</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">sketchSize</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">sketch</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">getKmerSize</span></span><span class="p"><span class="idiff">(),</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">sketch</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">getKmerSpace</span></span><span class="p"><span class="idiff">(),</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="mf" style="color: #099;"><span class="idiff">1.</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="mf" style="color: #099;"><span class="idiff right">1.</span></span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC210" class="line" lang="cpp">    <span class="idiff left">    </span><span class="n" style="color: #333;"><span class="idiff">compareSketches</span></span><span class="p"><span class="idiff">(</span></span><span class="o" style="font-weight: 600;"><span class="idiff">&</span></span><span class="n" style="color: #333;"><span class="idiff">output</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">pairs</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="p"><span class="idiff">],</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">sketch</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">getReference</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">input</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">index</span></span><span class="p"><span class="idiff">),</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">sketch</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">getReference</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="p"><span class="idiff">),</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">sketchSize</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">sketch</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">getKmerSize</span></span><span class="p"><span class="idiff">(),</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">sketch</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">getKmerSpace</span></span><span class="p"><span class="idiff">(),</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">input</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">maxDistance</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">input</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff right">maxPValue</span></span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="211" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC211" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="212" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC212" class="line" lang="cpp">    </span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="176" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="213" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC213" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">output</span><span class="p">;</span></span>

</pre>

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<br>

</li>

<li id="d02e98b4956e5520d320ab853dea3fc999d68ce8">

<a href="https://salsa.debian.org/med-team/mash/commit/5e14db80cf1008378399b328c70a9ff7b5c730e4#d02e98b4956e5520d320ab853dea3fc999d68ce8"><strong>src/mash/CommandTriangle.h</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -19,16 +19,20 @@ public:</td>

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19

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<td class="diff-line-num new_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

19

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<pre style="margin: 0;"> <span id="LC19" class="line" lang="c">    </span>

</pre>

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<pre style="margin: 0;"> <span id="LC20" class="line" lang="c">    <span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">TriangleInput</span></span>

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<pre style="margin: 0;"> <span id="LC21" class="line" lang="c">    <span class="p">{</span></span>

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<pre style="margin: 0;">-<span id="LC22" class="line" lang="c">        <span class="n" style="color: #333;">TriangleInput</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Sketch</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">sketchNew</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">indexNew</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Sketch</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Parameters</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">parametersNew</span><span class="p">)</span></span>

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<td class="diff-line-num new old_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC22" class="line" lang="c">        <span class="n" style="color: #333;">TriangleInput</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Sketch</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">sketchNew</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">indexNew</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Sketch</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Parameters</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">parametersNew</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">double</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">maxDistanceNew</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">double</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">maxPValueNew</span></span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC23" class="line" lang="c">            <span class="o" style="font-weight: 600;">:</span></span>

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<td class="diff-line-num old_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC24" class="line" lang="c">            <span class="n" style="color: #333;">sketch</span><span class="p">(</span><span class="n" style="color: #333;">sketchNew</span><span class="p">),</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC25" class="line" lang="c">            <span class="n" style="color: #333;">index</span><span class="p">(</span><span class="n" style="color: #333;">indexNew</span><span class="p">),</span></span>

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<pre style="margin: 0;">-<span id="LC26" class="line" lang="c">            <span class="n" style="color: #333;">parameters</span><span class="p">(</span><span class="n" style="color: #333;">parametersNew</span><span class="p">)</span></span>

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<td class="diff-line-num new old_line" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC26" class="line" lang="c">            <span class="n" style="color: #333;">parameters</span><span class="p">(</span><span class="n" style="color: #333;">parametersNew</span><span class="p">),</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC27" class="line" lang="c">            <span class="n" style="color: #333;">maxDistance</span><span class="p">(</span><span class="n" style="color: #333;">maxDistanceNew</span><span class="p">),</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC28" class="line" lang="c">            <span class="n" style="color: #333;">maxPValue</span><span class="p">(</span><span class="n" style="color: #333;">maxPValueNew</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC29" class="line" lang="c">            <span class="p">{}</span></span>

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<pre style="margin: 0;"> <span id="LC30" class="line" lang="c">        </span>

</pre>

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<pre style="margin: 0;"> <span id="LC31" class="line" lang="c">        <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Sketch</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">sketch</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC32" class="line" lang="c">        <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">index</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC33" class="line" lang="c">        <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Sketch</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Parameters</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">parameters</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC34" class="line" lang="c">        <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">maxDistance</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="35" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC35" class="line" lang="c">        <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">maxPValue</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC36" class="line" lang="c">    <span class="p">};</span></span>

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<pre style="margin: 0;"> <span id="LC37" class="line" lang="c">    </span>

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<pre style="margin: 0;"> <span id="LC38" class="line" lang="c">    <span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">TriangleOutput</span></span>

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<pre style="margin: 0;"> <span id="LC65" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">pValueMax</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC66" class="line" lang="c">    <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">comment</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC67" class="line" lang="c">    </span>

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<pre style="margin: 0;">-<span id="LC64" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">writeOutput</span><span class="p">(</span><span class="n" style="color: #333;">TriangleOutput</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">output</span><span class="p">,</span> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">comment</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">double</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">pValueMax</span></span><span class="p">)</span> <span class="k" style="font-weight: 600;">const</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC68" class="line" lang="c">    <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">writeOutput</span><span class="p">(</span><span class="n" style="color: #333;">TriangleOutput</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">output</span><span class="p">,</span> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">comment</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">bool</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">edge</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">double</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">pValuePeakToSet</span></span><span class="p">)</span> <span class="k" style="font-weight: 600;">const</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC69" class="line" lang="c"><span class="p">};</span></span>

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<pre style="margin: 0;"> <span id="LC70" class="line" lang="c"></span>

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<pre style="margin: 0;"> <span id="LC71" class="line" lang="c"><span class="n" style="color: #333;">CommandTriangle</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">TriangleOutput</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">compare</span><span class="p">(</span><span class="n" style="color: #333;">CommandTriangle</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">TriangleInput</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">input</span><span class="p">);</span></span>

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<li id="2ecd5edfb9906ffd092b9b8b4d28f6cb2eed2783">

<a href="https://salsa.debian.org/med-team/mash/commit/5e14db80cf1008378399b328c70a9ff7b5c730e4#2ecd5edfb9906ffd092b9b8b4d28f6cb2eed2783"><strong>src/mash/version.h</strong></a>

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<pre style="margin: 0;"> <span id="LC4" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">//</span></span>

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<pre style="margin: 0;"> <span id="LC5" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// See the LICENSE.txt file included with this software for license information.</span></span>

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<pre style="margin: 0;"> <span id="LC6" class="line" lang="c"></span>

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<pre style="margin: 0;">-<span id="LC7" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">version</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"2.<span class="idiff left right">1.1</span>"</span><span class="p">;</span></span></pre>

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">version</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"2.<span class="idiff left right">2</span>"</span><span class="p">;</span></span></pre>

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</li>

<li id="73531968fb1b31378d10ac3f11bf38fff6f7028c">

<a href="https://salsa.debian.org/med-team/mash/commit/5e14db80cf1008378399b328c70a9ff7b5c730e4#73531968fb1b31378d10ac3f11bf38fff6f7028c"><strong>test/ref/screen</strong></a>

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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">0.861792      44/1000 1       5.007<span class="idiff left right">39</span>e-229        genome1.fna     gi|49175990|ref|NC_000913.2| Escherichia coli str. K-12 substr. MG1655, complete genome</span>

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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">0.853596      36/1000 1       1.704<span class="idiff left right">79</span>e-184        genome2.fna     gi|47118301|dbj|BA000007.2| Escherichia coli O157:H7 str. Sakai DNA, complete genome</span>

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<td class="diff-line-num new_line old" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">0.861792      44/1000 1       5.007<span class="idiff left right">39</span>e-229        genome3.fna     gi|682117612|gb|CP009273.1| Escherichia coli BW25113, complete genome</span></pre>

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1

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">0.861792      44/1000 1       5.007<span class="idiff left right">42</span>e-229        genome1.fna     gi|49175990|ref|NC_000913.2| Escherichia coli str. K-12 substr. MG1655, complete genome</span>

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<td class="diff-line-num new new_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">0.853596      36/1000 1       1.704<span class="idiff left right">8</span>e-184 genome2.fna     gi|47118301|dbj|BA000007.2| Escherichia coli O157:H7 str. Sakai DNA, complete genome</span>

</pre>

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3

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">0.861792      44/1000 1       5.007<span class="idiff left right">42</span>e-229        genome3.fna     gi|682117612|gb|CP009273.1| Escherichia coli BW25113, complete genome</span></pre>

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