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<h3>
Steffen Möller pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/kma">Debian Med / kma</a>
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<h4>
Commits:
</h4>
<ul>
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<strong><a href="https://salsa.debian.org/med-team/kma/-/commit/2f19ae42ee0599842c05907229fbcefcd490ae07">2f19ae42</a></strong>
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<span>by Steffen Moeller</span>
<i>at 2020-05-14T17:49:12+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 1.2.25</pre>
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<h4>14 changed files:</h4>
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<li class="file-stats">
<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
README.md
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<li class="file-stats">
<a href="#66fff59064c69106947290d36caf080b8b637bfa">
ef.c
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<li class="file-stats">
<a href="#a6c1070a5546ad32dd5528a47f112252e946ab23">
hashtable.c
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<li class="file-stats">
<a href="#58c9ee503e2944f3ac7d5f5f5723c1784e1d61c8">
hashtable.h
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<li class="file-stats">
<a href="#5bb411548ec4b39482e6de83d3ad98f29b1162b1">
kma.c
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<li class="file-stats">
<a href="#24b1ddd54f1e7a0b2170af91261c0ecfa055c98d">
runinput.c
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<li class="file-stats">
<a href="#04f591434765972061a4501d514d48d8e013bc2a">
runinput.h
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<li class="file-stats">
<a href="#ca9efd475143efe0a1b0464c67f49900d98ca75a">
runkma.c
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<li class="file-stats">
<a href="#96f176d59b0bd765be8443801e2c6244ae632120">
runkma.h
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<li class="file-stats">
<a href="#cd8b7c197c9ac04f72eb54b22a8a01d5b1d0391f">
sparse.c
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<li class="file-stats">
<a href="#f8f573854be7916ca90c455745a849da49f628e3">
sparse.h
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<a href="#f80652dda49a7117428c0f92935664fc8cd4e2d1">
spltdb.c
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<a href="#e55b6b603fd8c696cd5ece7be98d78898a9ee58f">
spltdb.h
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<li class="file-stats">
<a href="#2d1dba06c7f4b4c2f13e05d40a391d5330c68ce4">
version.h
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<h4>Changes:</h4>
<li id="8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
<a href="https://salsa.debian.org/med-team/kma/-/commit/2f19ae42ee0599842c05907229fbcefcd490ae07#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d"><strong>README.md</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="markdown"><span class="gh" style="color: #999;"># Getting Started #</span></span><span class="idiff left right">
</span></pre>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="markdown"></span><span class="idiff left right">
</span></pre>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="markdown"><span class="p">```</span><span class="nl"></span></span><span class="idiff left right">
</span></pre>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="markdown">git clone https://bitbucket.org/genomicepidemiology/kma.git</span><span class="idiff left right">
</span></pre>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="markdown">cd kma && make</span><span class="idiff left right">
</span></pre>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="markdown"></span><span class="idiff left right">
</span></pre>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="markdown">./kma index -i templates.fsa.gz -o templates</span><span class="idiff left right">
</span></pre>
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<td class="diff-line-num old old_line" data-linenumber="8" style="width: 35px; color: rgba(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="LC8" class="line" lang="markdown">./kma -i reads_se.fq.gz -o output/name -t_db templates</span><span class="idiff left right">
</span></pre>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="markdown">./kma -ipe reads_1.fq.gz reads_2.fq.gz -o output/name -t_db templates</span><span class="idiff left right">
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="markdown"><span class="p">```</span></span><span class="idiff left right">
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="markdown"></span><span class="idiff left right">
</span></pre>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="markdown"><span class="gh" style="color: #999;"># Introduction #</span></span><span class="idiff left right">
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="markdown">KMA is a mapping method designed to map raw reads directly against redundant databases, in an </span><span class="idiff left right">
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="markdown">ultra-fast manner using seed and extend. KMA is particulary good at aligning </span><span class="idiff left right">
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="markdown">high quality reads against highly redundant databases, where unique matches often does </span><span class="idiff left right">
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="markdown">not exist. It works for long low quality reads as well, such as those from Nanopore. </span><span class="idiff left right">
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="markdown">Non-unique matches are resolved using the "ConClave" sorting scheme, and a consensus sequence are outputtet</span><span class="idiff left right">
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="markdown">in addition to other common attributes, based on our users demands.</span><span class="idiff left right">
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="markdown"></span><span class="idiff left right">
</span></pre>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="markdown">If you use KMA for your published research, then please cite:</span><span class="idiff left right">
</span></pre>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="markdown">Philip T.L.C. Clausen, Frank M. Aarestrup & Ole Lund, </span><span class="idiff left right">
</span></pre>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="markdown">"Rapid and precise alignment of raw reads against redundant databases with KMA", </span><span class="idiff left right">
</span></pre>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="markdown">BMC Bioinformatics, 2018;19:307.</span><span class="idiff left right">
</span></pre>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="markdown"></span><span class="idiff left right">
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="markdown"></span><span class="idiff left right">
</span></pre>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="markdown"><span class="gh" style="color: #999;"># Usage #</span></span><span class="idiff left right">
</span></pre>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="markdown">A more detailed guide on KMA and its options can be found in the pdf "KMAspecification.pdf".</span><span class="idiff left right">
</span></pre>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="markdown">For practical reasons you might want to add kma to your path, this is usually done with:</span><span class="idiff left right">
</span></pre>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="markdown"></span><span class="idiff left right">
</span></pre>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="markdown"><span class="p">```</span><span class="nl"></span></span><span class="idiff left right">
</span></pre>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="markdown">mv kma ~/bin/</span><span class="idiff left right">
</span></pre>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="markdown"><span class="p">```</span></span><span class="idiff left right">
</span></pre>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="markdown"></span><span class="idiff left right">
</span></pre>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Indexing ##</span></span><span class="idiff left right">
</span></pre>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="markdown">In order to use KMA for mapping, the databases need to indexed. </span><span class="idiff left right">
</span></pre>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="markdown">This is done with <span class="idiff left">“kma index”, the most important options are described below:</span></span><span class="idiff right">
</span></pre>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="markdown"></span><span class="idiff left right">
</span></pre>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="markdown"><span class="p">```</span><span class="nl"></span></span><span class="idiff left right">
</span></pre>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="markdown">-i Input fasta file(s), space separated. By default kma index reads from stdin.</span><span class="idiff left right">
</span></pre>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="markdown">-o Output name, the name given to the database.</span><span class="idiff left right">
</span></pre>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="markdown">-k kmersize used for indexing the database.</span><span class="idiff left right">
</span></pre>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="markdown">-k_t kmersize used to identify template candidates when running KMA.</span><span class="idiff left right">
</span></pre>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="markdown">-k_i kmersize used when performing alignments between two sequences.</span><span class="idiff left right">
</span></pre>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="markdown"><span class="p">```</span></span><span class="idiff left right">
</span></pre>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="markdown"></span><span class="idiff left right">
</span></pre>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="markdown">Example of use:</span><span class="idiff left right">
</span></pre>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="markdown"></span><span class="idiff left right">
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="markdown"><span class="p">```</span><span class="nl"></span></span><span class="idiff left right">
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="markdown">kma index -i templates.fsa.gz -o database/name</span><span class="idiff left right">
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="markdown"><span class="p">```</span></span><span class="idiff left right">
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="markdown"></span><span class="idiff left right">
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Mapping ##</span></span><span class="idiff left right">
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="markdown">The default settings of KMA is set so that it should work on most cases, </span><span class="idiff left right">
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="markdown">but it is evident to use the right options for the right problems.</span><span class="idiff left right">
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="markdown">Some of the most important options:</span><span class="idiff left right">
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="markdown"></span><span class="idiff left right">
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="markdown"><span class="p">```</span><span class="nl"></span></span><span class="idiff left right">
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="markdown">-i Inputfile(s), default is read from stdin. All input options takes as many files as you wish in fastq or fasta format, space separated.</span><span class="idiff left right">
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="markdown">-ipe Inputfile(s), paired end. The file pairs should be placed right after each other.</span><span class="idiff left right">
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="markdown">-int Inputfile(s), interleaved.</span><span class="idiff left right">
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="markdown">-o Output destination.</span><span class="idiff left right">
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="markdown">-t_db Database from indexing.</span><span class="idiff left right">
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="markdown">-mem_mode *.index and *.seq are not loaded into memory, which enables one to map against larger databases. Templates are chosen using k-mer counting.</span><span class="idiff left right">
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="markdown">-dense Skip insertions when making the consensus sequence.</span><span class="idiff left right">
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="markdown">-ref_fsa <span class="idiff left">“-” will be substituted with “n” in the consensus sequence.</span></span><span class="idiff right">
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<pre style="margin: 0;">-<span id="LC66" class="line" lang="markdown">-matrix Gives the counts all all called bases at each position in each mapped template. Columns are: reference base, A count, C count, G count, T count, N count, - count.</span><span class="idiff left right">
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="markdown">-mp Minimum phred-score.</span><span class="idiff left right">
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<pre style="margin: 0;">-<span id="LC68" class="line" lang="markdown">-Mt1 Match to only one template in the database.</span><span class="idiff left right">
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="markdown">-ID Minimum identity to output template match.</span><span class="idiff left right">
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="markdown">-apm Paired end method, <span class="idiff left">“p”: Reward if pairing the reads, “u”: unite best template matches in each read if possible, “f” force paired reads to pair.</span></span><span class="idiff right">
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="markdown">-1t1 One read to one template, no splicing performed. Well suited for short reads and whole genome mapping.</span><span class="idiff left right">
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="markdown">-bc90 Basecalls should be significantly overrepresented, and have at least 90% agreement.</span><span class="idiff left right">
</span></pre>
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<pre style="margin: 0;">-<span id="LC73" class="line" lang="markdown">-bcNano Basecalls optimized for nanopore sequencing.</span><span class="idiff left right">
</span></pre>
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<pre style="margin: 0;">-<span id="LC74" class="line" lang="markdown">-mrs minimum alignment score normalized to alignment length.</span><span class="idiff left right">
</span></pre>
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<pre style="margin: 0;">-<span id="LC75" class="line" lang="markdown"><span class="p">```</span></span><span class="idiff left right">
</span></pre>
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<pre style="margin: 0;">-<span id="LC76" class="line" lang="markdown"></span><span class="idiff left right">
</span></pre>
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<pre style="margin: 0;">-<span id="LC77" class="line" lang="markdown">Examples of running KMA:</span><span class="idiff left right">
</span></pre>
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78
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<pre style="margin: 0;">-<span id="LC78" class="line" lang="markdown"></span><span class="idiff left right">
</span></pre>
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<pre style="margin: 0;">-<span id="LC79" class="line" lang="markdown">Short read mapping, one read maps only to one template:</span><span class="idiff left right">
</span></pre>
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80
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<pre style="margin: 0;">-<span id="LC80" class="line" lang="markdown"><span class="p">```</span><span class="nl"></span></span><span class="idiff left right">
</span></pre>
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<pre style="margin: 0;">-<span id="LC81" class="line" lang="markdown">kma <span class="idiff left">–i singleEndReads.fq.gz –ipe pairedEnd_*.fq.gz –o output/name –t_db database/name -1t1</span></span><span class="idiff right">
</span></pre>
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82
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<pre style="margin: 0;">-<span id="LC82" class="line" lang="markdown"><span class="p">```</span></span><span class="idiff left right">
</span></pre>
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83
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<pre style="margin: 0;">-<span id="LC83" class="line" lang="markdown"></span><span class="idiff left right">
</span></pre>
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<pre style="margin: 0;">-<span id="LC84" class="line" lang="markdown">Long read mapping against a database of genes:</span><span class="idiff left right">
</span></pre>
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85
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<pre style="margin: 0;">-<span id="LC85" class="line" lang="markdown"><span class="p">```</span><span class="nl"></span></span><span class="idiff left right">
</span></pre>
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<pre style="margin: 0;">-<span id="LC86" class="line" lang="markdown">kma <span class="idiff left">–i someLongReads.fq.gz –o output/name –t_db database/name</span></span><span class="idiff right">
</span></pre>
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87
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<pre style="margin: 0;">-<span id="LC87" class="line" lang="markdown"><span class="p">```</span></span><span class="idiff left right">
</span></pre>
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88
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<pre style="margin: 0;">-<span id="LC88" class="line" lang="markdown"></span><span class="idiff left right">
</span></pre>
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89
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<pre style="margin: 0;">-<span id="LC89" class="line" lang="markdown">Whole genome mapping with nanopore reads:</span><span class="idiff left right">
</span></pre>
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90
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<pre style="margin: 0;">-<span id="LC90" class="line" lang="markdown"><span class="p">```</span><span class="nl"></span></span><span class="idiff left right">
</span></pre>
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91
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<pre style="margin: 0;">-<span id="LC91" class="line" lang="markdown">kma <span class="idiff left">–i nanoporeReads.fq.gz –o output/name –t_db database/name –mem_mode –mp 20 –mrs 0.0 –bcNano</span></span><span class="idiff right">
</span></pre>
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92
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<pre style="margin: 0;">-<span id="LC92" class="line" lang="markdown"><span class="p">```</span></span><span class="idiff left right">
</span></pre>
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93
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<pre style="margin: 0;">-<span id="LC93" class="line" lang="markdown"></span><span class="idiff left right">
</span></pre>
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94
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<pre style="margin: 0;">-<span id="LC94" class="line" lang="markdown">Whole genome mapping against a single genome in the database (still nanopore), specified by template number (here <span class="idiff left">“2”).</span></span><span class="idiff right">
</span></pre>
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95
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<pre style="margin: 0;">-<span id="LC95" class="line" lang="markdown">This is the same as the line number of the wanted sequences in the <span class="se" style="color: #d14;">\*</span>.name file from the indexing.</span><span class="idiff left right">
</span></pre>
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<pre style="margin: 0;">-<span id="LC96" class="line" lang="markdown"><span class="p">```</span><span class="nl"></span></span><span class="idiff left right">
</span></pre>
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<td class="diff-line-num old old_line" data-linenumber="97" style="width: 35px; color: rgba(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="LC97" class="line" lang="markdown">kma <span class="idiff left">–i nanoporeReads.fq.gz –o output/name –t_db database/name –mp 20 –mrs 0.0 –bcNano –Mt1 2</span></span><span class="idiff right">
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<pre style="margin: 0;">-<span id="LC98" class="line" lang="markdown"><span class="p">```</span></span><span class="idiff left right">
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<pre style="margin: 0;">-<span id="LC99" class="line" lang="markdown"></span><span class="idiff left right">
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<pre style="margin: 0;">-<span id="LC100" class="line" lang="markdown"></span><span class="idiff left right">
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<pre style="margin: 0;">-<span id="LC101" class="line" lang="markdown"><span class="gh" style="color: #999;"># Result Explanation #</span></span><span class="idiff left right">
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<pre style="margin: 0;">-<span id="LC102" class="line" lang="markdown">When the mapping is done KMA will produce the following files:</span><span class="idiff left right">
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<pre style="margin: 0;">-<span id="LC103" class="line" lang="markdown"><span class="p"></span></span><span class="idiff left right">
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<pre style="margin: 0;">-<span id="LC104" class="line" lang="markdown"><span class="p">1.</span> <span class="se" style="color: #d14;">\*</span>.res A result overview giving the most common statistics for each mapped template.</span><span class="idiff left right">
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<pre style="margin: 0;">-<span id="LC105" class="line" lang="markdown"><span class="p">2.</span> <span class="se" style="color: #d14;">\*</span>.fsa The consensus sequences drawn from the alignments.</span><span class="idiff left right">
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<pre style="margin: 0;">-<span id="LC106" class="line" lang="markdown"><span class="p">3.</span> <span class="se" style="color: #d14;">\*</span>.aln The consensus alignment of the reads against their template.</span><span class="idiff left right">
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<pre style="margin: 0;">-<span id="LC107" class="line" lang="markdown"><span class="p">4.</span> <span class="se" style="color: #d14;">\*</span>.frag.gz Mapping information on each mapped read, columns are: read, number of equally well mapping templates, mapping score, start position, end position (w.r.t. template), the choosen template.</span><span class="idiff left right">
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<pre style="margin: 0;">-<span id="LC108" class="line" lang="markdown"><span class="p">5.</span> <span class="se" style="color: #d14;">\*</span>.mat.gz Base counts on each position in each template, (only if <span class="idiff left">“-matrix” is enabled)</span></span><span class="idiff right">
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<pre style="margin: 0;">-<span id="LC109" class="line" lang="markdown"></span><span class="idiff left right">
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<pre style="margin: 0;">-<span id="LC110" class="line" lang="markdown"><span class="gh" style="color: #999;"># Shared memory #</span></span><span class="idiff left right">
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<pre style="margin: 0;">-<span id="LC111" class="line" lang="markdown">The databases of KMA can be put into shared memory, this enables you to align several </span><span class="idiff left right">
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<pre style="margin: 0;">-<span id="LC112" class="line" lang="markdown">samples at ones while only having the database loaded in one place. </span><span class="idiff left right">
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<pre style="margin: 0;">-<span id="LC113" class="line" lang="markdown">KMA_SHM can be used to put the databases into shared memory, and most importantly take them </span><span class="idiff left right">
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<pre style="margin: 0;">-<span id="LC114" class="line" lang="markdown">down afterwards. It is of the highest concern that these shared databases are used correctly, </span><span class="idiff left right">
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<pre style="margin: 0;">-<span id="LC115" class="line" lang="markdown">as they will take up a part of memory and they will exist there until they are taken down again, </span><span class="idiff left right">
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<pre style="margin: 0;">-<span id="LC116" class="line" lang="markdown">the computer is restarted or computer breaks down.</span><span class="idiff left right">
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<pre style="margin: 0;">-<span id="LC117" class="line" lang="markdown"></span><span class="idiff left right">
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<pre style="margin: 0;">-<span id="LC118" class="line" lang="markdown">Example of setting up a database in shared memory.</span><span class="idiff left right">
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<pre style="margin: 0;">-<span id="LC119" class="line" lang="markdown"><span class="p">```</span><span class="nl"></span></span><span class="idiff left right">
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<pre style="margin: 0;">-<span id="LC120" class="line" lang="markdown">kma shm <span class="idiff left">–t_db templates –shmLvl 1</span></span><span class="idiff right">
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<pre style="margin: 0;">-<span id="LC121" class="line" lang="markdown"><span class="p">```</span></span><span class="idiff left right">
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<pre style="margin: 0;">-<span id="LC122" class="line" lang="markdown"></span><span class="idiff left right">
</span></pre>
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<pre style="margin: 0;">-<span id="LC123" class="line" lang="markdown"><span class="idiff left">“-shmLvl” specifies how much of the database there should be stored in shared memory, use.</span></span><span class="idiff right">
</span></pre>
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<pre style="margin: 0;">-<span id="LC124" class="line" lang="markdown"><span class="idiff left">“-shm-h” to get an overview of the different levels.</span></span><span class="idiff right">
</span></pre>
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<pre style="margin: 0;">-<span id="LC125" class="line" lang="markdown"></span><span class="idiff left right">
</span></pre>
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126
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<pre style="margin: 0;">-<span id="LC126" class="line" lang="markdown">Example of taking it down again, always remember to do this then it is no longer needed:</span><span class="idiff left right">
</span></pre>
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127
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<pre style="margin: 0;">-<span id="LC127" class="line" lang="markdown"><span class="p">```</span><span class="nl"></span></span><span class="idiff left right">
</span></pre>
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128
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<pre style="margin: 0;">-<span id="LC128" class="line" lang="markdown">kma shm <span class="idiff left">–t_db database/name –shmLvl 1 –destroy</span></span><span class="idiff right">
</span></pre>
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129
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<pre style="margin: 0;">-<span id="LC129" class="line" lang="markdown"><span class="p">```</span></span><span class="idiff left right">
</span></pre>
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130
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<pre style="margin: 0;">-<span id="LC130" class="line" lang="markdown"></span><span class="idiff left right">
</span></pre>
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131
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<pre style="margin: 0;">-<span id="LC131" class="line" lang="markdown"><span class="gh" style="color: #999;"># Installation Requirements #</span></span><span class="idiff left right">
</span></pre>
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132
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<pre style="margin: 0;">-<span id="LC132" class="line" lang="markdown">In order to install KMA, you need to have a C-compiler and zlib development files installed.</span><span class="idiff left right">
</span></pre>
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133
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<pre style="margin: 0;">-<span id="LC133" class="line" lang="markdown">Zlib development files can be installed on unix systems with:</span><span class="idiff left right">
</span></pre>
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134
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<pre style="margin: 0;">-<span id="LC134" class="line" lang="markdown"><span class="p">```</span><span class="nl"></span></span><span class="idiff left right">
</span></pre>
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135
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<pre style="margin: 0;">-<span id="LC135" class="line" lang="markdown">sudo apt-get install libz-dev</span><span class="idiff left right">
</span></pre>
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136
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<pre style="margin: 0;">-<span id="LC136" class="line" lang="markdown"><span class="p">```</span></span><span class="idiff left right">
</span></pre>
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137
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<pre style="margin: 0;">-<span id="LC137" class="line" lang="markdown"></span><span class="idiff left right">
</span></pre>
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138
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<pre style="margin: 0;">-<span id="LC138" class="line" lang="markdown"><span class="gh" style="color: #999;"># Help #</span></span><span class="idiff left right">
</span></pre>
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139
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<pre style="margin: 0;">-<span id="LC139" class="line" lang="markdown">Usage and options are available with the "-h" option on all three programs.</span><span class="idiff left right">
</span></pre>
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140
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<pre style="margin: 0;">-<span id="LC140" class="line" lang="markdown">If in doubt, please mail any concerns or problems to: <span class="ge" style="font-style: italic;">*plan@dtu.dk*</span>.</span><span class="idiff left right">
</span></pre>
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<td class="diff-line-num old old_line" data-linenumber="141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
141
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<pre style="margin: 0;">-<span id="LC141" class="line" lang="markdown"></span><span class="idiff left right">
</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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<pre style="margin: 0;">-<span id="LC142" class="line" lang="markdown"><span class="gh" style="color: #999;"># Citation #</span></span><span class="idiff left right">
</span></pre>
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143
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<pre style="margin: 0;">-<span id="LC143" class="line" lang="markdown"><span class="p">1.</span> Philip T.L.C. Clausen, Frank M. Aarestrup & Ole Lund, "Rapid and precise alignment of raw reads against redundant databases with KMA", BMC Bioinformatics, 2018;19:307.</span><span class="idiff left right">
</span></pre>
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144
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<pre style="margin: 0;">-<span id="LC144" class="line" lang="markdown"></span><span class="idiff left right">
</span></pre>
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145
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<pre style="margin: 0;">-<span id="LC145" class="line" lang="markdown"><span class="gh" style="color: #999;"># License #</span></span><span class="idiff left right">
</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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<pre style="margin: 0;">-<span id="LC146" class="line" lang="markdown">Copyright (c) 2017, Philip Clausen, Technical University of Denmark</span><span class="idiff left right">
</span></pre>
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<pre style="margin: 0;">-<span id="LC147" class="line" lang="markdown">All rights reserved.</span><span class="idiff left right">
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<pre style="margin: 0;">-<span id="LC148" class="line" lang="markdown"></span><span class="idiff left right">
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<pre style="margin: 0;">-<span id="LC149" class="line" lang="markdown">Licensed under the Apache License, Version 2.0 (the "License");</span><span class="idiff left right">
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150
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<pre style="margin: 0;">-<span id="LC150" class="line" lang="markdown">you may not use this file except in compliance with the License.</span><span class="idiff left right">
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151
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<pre style="margin: 0;">-<span id="LC151" class="line" lang="markdown">You may obtain a copy of the License at</span><span class="idiff left right">
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152
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<pre style="margin: 0;">-<span id="LC152" class="line" lang="markdown"></span><span class="idiff left right">
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153
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<pre style="margin: 0;">-<span id="LC153" class="line" lang="markdown"> http://www.apache.org/licenses/LICENSE-2.0</span><span class="idiff left right">
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154
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<pre style="margin: 0;">-<span id="LC154" class="line" lang="markdown"></span><span class="idiff left right">
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155
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<pre style="margin: 0;">-<span id="LC155" class="line" lang="markdown">Unless required by applicable law or agreed to in writing, software</span><span class="idiff left right">
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156
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<pre style="margin: 0;">-<span id="LC156" class="line" lang="markdown">distributed under the License is distributed on an "AS IS" BASIS,</span><span class="idiff left right">
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157
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<pre style="margin: 0;">-<span id="LC157" class="line" lang="markdown">WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.</span><span class="idiff left right">
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158
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<pre style="margin: 0;">-<span id="LC158" class="line" lang="markdown">See the License for the specific language governing permissions and</span><span class="idiff left right">
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159
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<pre style="margin: 0;">-<span id="LC159" class="line" lang="markdown">limitations under the License.</span><span class="idiff left right"></span></pre>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="markdown"><span class="gh" style="color: #999;"># Getting Started #</span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="markdown"></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="markdown"><span class="p">```</span></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="markdown">git clone https://bitbucket.org/genomicepidemiology/kma.git</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="markdown">cd kma && make</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="markdown"></span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="markdown">./kma index -i templates.fsa.gz -o templates</span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="markdown">./kma -i reads_se.fq.gz -o output/name -t_db templates</span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="markdown">./kma -ipe reads_1.fq.gz reads_2.fq.gz -o output/name -t_db templates</span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="markdown"><span class="p">```</span></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="markdown"></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="markdown"><span class="gh" style="color: #999;"># Introduction #</span></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="markdown">KMA is a mapping method designed to map raw reads directly against redundant databases, in an </span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="markdown">ultra-fast manner using seed and extend. KMA is particulary good at aligning </span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="markdown">high quality reads against highly redundant databases, where unique matches often does </span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="markdown">not exist. It works for long low quality reads as well, such as those from Nanopore. </span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="markdown">Non-unique matches are resolved using the "ConClave" sorting scheme, and a consensus sequence are outputtet</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="markdown">in addition to other common attributes, based on our users demands.</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="markdown">If you use KMA for your published research, then please cite:</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="markdown">Philip T.L.C. Clausen, Frank M. Aarestrup & Ole Lund, </span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="markdown">"Rapid and precise alignment of raw reads against redundant databases with KMA", </span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="markdown">BMC Bioinformatics, 2018;19:307.</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="markdown"><span class="gh" style="color: #999;"># Usage #</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="markdown">A more detailed guide on KMA and its options can be found in the pdf "KMAspecification.pdf".</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="markdown">For practical reasons you might want to add kma to your path, this is usually done with:</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="markdown">mv kma ~/bin/</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Indexing ##</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="markdown">In order to use KMA for mapping, the databases need to indexed. </span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="markdown">This is done with <span class="idiff left right">kma index, the most important options are described below:</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="markdown">-i Input fasta file(s), space separated. By default kma index reads from stdin.</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="markdown">-o Output name, the name given to the database.</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="markdown">-k kmersize used for indexing the database.</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="markdown">-k_t kmersize used to identify template candidates when running KMA.</span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="markdown">-k_i kmersize used when performing alignments between two sequences.</span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="markdown">Example of use:</span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="markdown">kma index -i templates.fsa.gz -o database/name</span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Mapping ##</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="markdown">The default settings of KMA is set so that it should work on most cases, </span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="markdown">but it is evident to use the right options for the right problems.</span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="markdown">Some of the most important options:</span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="markdown">-i Inputfile(s), default is read from stdin. All input options takes as many files as you wish in fastq or fasta format, space separated.</span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="markdown">-ipe Inputfile(s), paired end. The file pairs should be placed right after each other.</span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="markdown">-int Inputfile(s), interleaved.</span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="markdown">-o Output destination.</span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="markdown">-t_db Database from indexing.</span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="markdown">-mem_mode *.index and *.seq are not loaded into memory, which enables one to map against larger databases. Templates are chosen using k-mer counting.</span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="markdown">-dense Skip insertions when making the consensus sequence.</span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="markdown">-ref_fsa <span class="idiff left right">- will be substituted with n in the consensus sequence.</span></span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="markdown">-matrix Gives the counts all all called bases at each position in each mapped template. Columns are: reference base, A count, C count, G count, T count, N count, - count.</span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="markdown">-mp Minimum phred-score.</span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="markdown">-Mt1 Match to only one template in the database.</span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="markdown">-ID Minimum identity to output template match.</span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="markdown">-apm Paired end method, <span class="idiff left right">p: Reward if pairing the reads, u: unite best template matches in each read if possible, f force paired reads to pair.</span></span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="markdown">-1t1 One read to one template, no splicing performed. Well suited for short reads and whole genome mapping.</span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="markdown">-bc90 Basecalls should be significantly overrepresented, and have at least 90% agreement.</span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="markdown">-bcNano Basecalls optimized for nanopore sequencing.</span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="markdown">-mrs minimum alignment score normalized to alignment length.</span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="markdown">Examples of running KMA:</span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="markdown">Short read mapping, one read maps only to one template:</span>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="markdown">kma <span class="idiff left right">-i singleEndReads.fq.gz -ipe pairedEnd_*.fq.gz -o output/name -t_db database/name -1t1</span></span>
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="markdown">Long read mapping against a database of genes:</span>
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="markdown">kma <span class="idiff left right">-i someLongReads.fq.gz -o output/name -t_db database/name -bcNano -bc 0.7</span></span>
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="markdown">Whole genome mapping with nanopore reads:</span>
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="markdown">kma <span class="idiff left right">-i nanoporeReads.fq.gz -o output/name -t_db database/name -mem_mode -mp 20 -mrs 0.0 -bcNano -bc 0.7</span></span>
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="markdown">Whole genome mapping against a single genome in the database (still nanopore), specified by template number (here <span class="idiff left right">2).</span></span>
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="markdown">This is the same as the line number of the wanted sequences in the <span class="se" style="color: #d14;">\*</span>.name file from the indexing.</span>
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="markdown">kma <span class="idiff left right">-i nanoporeReads.fq.gz -o output/name -t_db database/name -mp 20 -bcNano -bc 0.7 -Mt1 2</span></span>
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="markdown"><span class="gh" style="color: #999;"># Result Explanation #</span></span>
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="markdown">When the mapping is done KMA will produce the following files:</span>
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="markdown"><span class="p">1.</span> <span class="se" style="color: #d14;">\*</span>.res A result overview giving the most common statistics for each mapped template.</span>
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="markdown"><span class="p">2.</span> <span class="se" style="color: #d14;">\*</span>.fsa The consensus sequences drawn from the alignments.</span>
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="markdown"><span class="p">3.</span> <span class="se" style="color: #d14;">\*</span>.aln The consensus alignment of the reads against their template.</span>
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="markdown"><span class="p">4.</span> <span class="se" style="color: #d14;">\*</span>.frag.gz Mapping information on each mapped read, columns are: read, number of equally well mapping templates, mapping score, start position, end position (w.r.t. template), the choosen template.</span>
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="markdown"><span class="p">5.</span> <span class="se" style="color: #d14;">\*</span>.mat.gz Base counts on each position in each template, (only if <span class="idiff left right">-matrix is enabled)</span></span>
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="markdown"><span class="gh" style="color: #999;"># Shared memory #</span></span>
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="markdown">The databases of KMA can be put into shared memory, this enables you to align several </span>
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="markdown">samples at ones while only having the database loaded in one place. </span>
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="markdown">KMA_SHM can be used to put the databases into shared memory, and most importantly take them </span>
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="markdown">down afterwards. It is of the highest concern that these shared databases are used correctly, </span>
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="markdown">as they will take up a part of memory and they will exist there until they are taken down again, </span>
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="markdown">the computer is restarted or computer breaks down.</span>
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="markdown">Example of setting up a database in shared memory.</span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="markdown">kma shm <span class="idiff left right">-t_db database/name -shmLvl 1</span></span>
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="markdown"><span class="p">```</span></span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="markdown"><span class="idiff left right">-shmLvl specifies how much of the database there should be stored in shared memory, use.</span></span>
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124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="markdown"><span class="idiff left right">-shm-h to get an overview of the different levels.</span></span>
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125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="markdown">Example of taking it down again, always remember to do this then it is no longer needed:</span>
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="markdown">kma shm <span class="idiff left right">-t_db database/name -shmLvl 1 -destroy</span></span>
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="markdown"><span class="p">```</span></span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="markdown"><span class="gh" style="color: #999;"># Installation Requirements #</span></span>
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="markdown">In order to install KMA, you need to have a C-compiler and zlib development files installed.</span>
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="markdown">Zlib development files can be installed on unix systems with:</span>
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="markdown">sudo apt-get install libz-dev</span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="markdown"><span class="p">```</span></span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="markdown"></span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="markdown"><span class="gh" style="color: #999;"># Help #</span></span>
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="markdown">Usage and options are available with the "-h" option on all three programs.</span>
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="markdown">If in doubt, please mail any concerns or problems to: <span class="ge" style="font-style: italic;">*plan@dtu.dk*</span>.</span>
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="markdown"><span class="gh" style="color: #999;"># Citation #</span></span>
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="markdown"><span class="p">1.</span> Philip T.L.C. Clausen, Frank M. Aarestrup & Ole Lund, "Rapid and precise alignment of raw reads against redundant databases with KMA", BMC Bioinformatics, 2018;19:307.</span>
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="markdown"><span class="gh" style="color: #999;"># License #</span></span>
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="markdown">Copyright (c) 2017, Philip Clausen, Technical University of Denmark</span>
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="markdown">All rights reserved.</span>
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="markdown">Licensed under the Apache License, Version 2.0 (the "License");</span>
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="markdown">You may obtain a copy of the License at</span>
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="markdown"><span class="sb" style="color: #d14;"> http://www.apache.org/licenses/LICENSE-2.0</span></span>
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="markdown">Unless required by applicable law or agreed to in writing, software</span>
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="markdown">distributed under the License is distributed on an "AS IS" BASIS,</span>
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="markdown">See the License for the specific language governing permissions and</span>
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="markdown">limitations under the License.</span></pre>
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<li id="66fff59064c69106947290d36caf080b8b637bfa">
<a href="https://salsa.debian.org/med-team/kma/-/commit/2f19ae42ee0599842c05907229fbcefcd490ae07#66fff59064c69106947290d36caf080b8b637bfa"><strong>ef.c</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">@@ -51,6 +51,7 @@ void getExtendedFeatures(char *template_name, AssemInfo *matrix, long unsigned *</td>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">var</span><span class="p">,</span> <span class="n" style="color: #333;">nucHighVar</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="c"> <span class="n" style="color: #333;">Assembly</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">assembly</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="c"> </span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="c"> <span class="n" style="color: #333;">fragmentCountAln</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(((</span><span class="n" style="color: #333;">readCountAln</span> <span class="o" style="font-weight: 600;">>></span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="n" style="color: #333;">readCountAln</span> <span class="o" style="font-weight: 600;">&</span> <span class="mi" style="color: #099;">1</span><span class="p">))</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">fragmentCountAln</span><span class="p">)</span> <span class="o" style="font-weight: 600;">?</span> <span class="p">(</span><span class="n" style="color: #333;">fragmentCountAln</span><span class="p">)</span> <span class="o" style="font-weight: 600;">:</span> <span class="p">((</span><span class="n" style="color: #333;">readCountAln</span> <span class="o" style="font-weight: 600;">>></span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="n" style="color: #333;">readCountAln</span> <span class="o" style="font-weight: 600;">&</span> <span class="mi" style="color: #099;">1</span><span class="p">));</span></span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">matrix</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* iterate matrix to get:</span></span>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> Nuc_high_depth_variance</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">@@ -34,7 +34,7 @@ int intpos_bin(const unsigned *str1, const int str2) {</td>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="c"> <span class="n" style="color: #333;">downLim</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="c"> <span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">upLim</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">downLim</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><span class="idiff left">/</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">2</span></span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="c"> <span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">upLim</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">downLim</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><span class="idiff left">>></span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">1</span></span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="c"> <span class="k" style="font-weight: 600;">while</span><span class="p">(</span><span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;"><</span> <span class="p">(</span><span class="n" style="color: #333;">upLim</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">downLim</span><span class="p">))</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">str1</span><span class="p">[</span><span class="n" style="color: #333;">pos</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">str2</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">pos</span><span class="p">;</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -43,7 +43,7 @@ int intpos_bin(const unsigned *str1, const int str2) {</td>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="c"> <span class="n" style="color: #333;">upLim</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="c"> <span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">upLim</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">downLim</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><span class="idiff left">/</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">2</span></span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="c"> <span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">upLim</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">downLim</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><span class="idiff left">>></span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">1</span></span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">str1</span><span class="p">[</span><span class="n" style="color: #333;">pos</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">str2</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">pos</span><span class="p">;</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -51,7 +51,7 @@ int intpos_bin(const unsigned *str1, const int str2) {</td>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="c"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="c"><span class="n" style="color: #333;">HashTable</span> <span class="o" style="font-weight: 600;">*</span> <span class="nf" style="color: #900; font-weight: 600;">collect_Kmers</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">HashMapKMA</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">templates</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">Scores</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">Scores_tot</span><span class="p">,</span> <span class="n" style="color: #333;">HashMap_kmers</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">foundKmers</span><span class="p">,</span> <span class="n" style="color: #333;">Hit</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">hits</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="c"><span class="n" style="color: #333;">HashTable</span> <span class="o" style="font-weight: 600;">*</span> <span class="nf" style="color: #900; font-weight: 600;">collect_Kmers</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">HashMapKMA</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">templates</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">Scores</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">long</span></span><span class="idiff right"> </span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">Scores_tot</span><span class="p">,</span> <span class="n" style="color: #333;">HashMap_kmers</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">foundKmers</span><span class="p">,</span> <span class="n" style="color: #333;">Hit</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">hits</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">template</span><span class="p">,</span> <span class="n" style="color: #333;">SU</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">j</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">value</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">@@ -118,7 +118,7 @@ HashTable * collect_Kmers(const HashMapKMA *templates, unsigned *Scores, unsigne</td>
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<pre style="margin: 0;"> <span id="LC118" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">kmerList</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC119" class="line" lang="c"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC120" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC121" class="line" lang="c"><span class="n" style="color: #333;">HashTable</span> <span class="o" style="font-weight: 600;">**</span> <span class="nf" style="color: #900; font-weight: 600;">collect_Kmers_deCon</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">HashMapKMA</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">templates</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">Scores</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">Scores_tot</span><span class="p">,</span> <span class="n" style="color: #333;">HashMap_kmers</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">foundKmers</span><span class="p">,</span> <span class="n" style="color: #333;">Hit</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">hits</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">contamination</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="c"><span class="n" style="color: #333;">HashTable</span> <span class="o" style="font-weight: 600;">**</span> <span class="nf" style="color: #900; font-weight: 600;">collect_Kmers_deCon</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">HashMapKMA</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">templates</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">Scores</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">long</span></span><span class="idiff right"> </span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">Scores_tot</span><span class="p">,</span> <span class="n" style="color: #333;">HashMap_kmers</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">foundKmers</span><span class="p">,</span> <span class="n" style="color: #333;">Hit</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">hits</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">contamination</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC122" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC123" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">template</span><span class="p">,</span> <span class="n" style="color: #333;">SU</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC124" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">j</span><span class="p">,</span> <span class="n" style="color: #333;">n</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">value</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">@@ -219,7 +219,7 @@ HashTable ** collect_Kmers_deCon(const HashMapKMA *templates, unsigned *Scores,</td>
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<pre style="margin: 0;"> <span id="LC219" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">Returner</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC220" class="line" lang="c"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC221" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC222" class="line" lang="c"><span class="n" style="color: #333;">HashTable</span> <span class="o" style="font-weight: 600;">*</span> <span class="nf" style="color: #900; font-weight: 600;">withDraw_Kmers</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">Scores</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">Scores_tot</span><span class="p">,</span> <span class="n" style="color: #333;">HashTable</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">kmerList</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">template</span><span class="p">,</span> <span class="n" style="color: #333;">Hit</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">hits</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="c"><span class="n" style="color: #333;">HashTable</span> <span class="o" style="font-weight: 600;">*</span> <span class="nf" style="color: #900; font-weight: 600;">withDraw_Kmers</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">Scores</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">long</span></span><span class="idiff right"> </span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">Scores_tot</span><span class="p">,</span> <span class="n" style="color: #333;">HashTable</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">kmerList</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">template</span><span class="p">,</span> <span class="n" style="color: #333;">Hit</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">hits</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC223" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC224" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">i</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC225" class="line" lang="c"> <span class="n" style="color: #333;">HashTable</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">node</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">prev</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="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="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -267,7 +267,7 @@ HashTable * withDraw_Kmers(unsigned *Scores, unsigned *Scores_tot, HashTable *km</td>
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<pre style="margin: 0;"> <span id="LC267" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">kmerList</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC268" class="line" lang="c"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC269" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC270" class="line" lang="c"><span class="n" style="color: #333;">Hit</span> <span class="nf" style="color: #900; font-weight: 600;">withDraw_Contamination</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">Scores</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">Scores_tot</span><span class="p">,</span> <span class="n" style="color: #333;">HashTable</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">kmerList</span><span class="p">,</span> <span class="n" style="color: #333;">HashTable</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">deConTable</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">template</span><span class="p">,</span> <span class="n" style="color: #333;">Hit</span> <span class="n" style="color: #333;">hits</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC270" class="line" lang="c"><span class="n" style="color: #333;">Hit</span> <span class="nf" style="color: #900; font-weight: 600;">withDraw_Contamination</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">Scores</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">long</span></span><span class="idiff right"> </span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">Scores_tot</span><span class="p">,</span> <span class="n" style="color: #333;">HashTable</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">kmerList</span><span class="p">,</span> <span class="n" style="color: #333;">HashTable</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">deConTable</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">template</span><span class="p">,</span> <span class="n" style="color: #333;">Hit</span> <span class="n" style="color: #333;">hits</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC271" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC272" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">belong</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC273" class="line" lang="c"> <span class="n" style="color: #333;">HashTable</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">node</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">prev</span><span class="p">;</span></span>
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<a href="https://salsa.debian.org/med-team/kma/-/commit/2f19ae42ee0599842c05907229fbcefcd490ae07#58c9ee503e2944f3ac7d5f5f5723c1784e1d61c8"><strong>hashtable.h</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -38,7 +38,7 @@ struct hit {</td>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">intpos_bin</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">str1</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">str2</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="c"><span class="n" style="color: #333;">HashTable</span> <span class="o" style="font-weight: 600;">*</span> <span class="nf" style="color: #900; font-weight: 600;">collect_Kmers</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">HashMapKMA</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">templates</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">Scores</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">Scores_tot</span><span class="p">,</span> <span class="n" style="color: #333;">HashMap_kmers</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">foundKmers</span><span class="p">,</span> <span class="n" style="color: #333;">Hit</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">hits</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="c"><span class="n" style="color: #333;">HashTable</span> <span class="o" style="font-weight: 600;">**</span> <span class="nf" style="color: #900; font-weight: 600;">collect_Kmers_deCon</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">HashMapKMA</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">templates</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">Scores</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">Scores_tot</span><span class="p">,</span> <span class="n" style="color: #333;">HashMap_kmers</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">foundKmers</span><span class="p">,</span> <span class="n" style="color: #333;">Hit</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">hits</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">contamination</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="c"><span class="n" style="color: #333;">HashTable</span> <span class="o" style="font-weight: 600;">*</span> <span class="nf" style="color: #900; font-weight: 600;">withDraw_Kmers</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">Scores</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">Scores_tot</span><span class="p">,</span> <span class="n" style="color: #333;">HashTable</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">kmerList</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">template</span><span class="p">,</span> <span class="n" style="color: #333;">Hit</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">hits</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="c"><span class="n" style="color: #333;">Hit</span> <span class="nf" style="color: #900; font-weight: 600;">withDraw_Contamination</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">Scores</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">Scores_tot</span><span class="p">,</span> <span class="n" style="color: #333;">HashTable</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">kmerList</span><span class="p">,</span> <span class="n" style="color: #333;">HashTable</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">deConTable</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">template</span><span class="p">,</span> <span class="n" style="color: #333;">Hit</span> <span class="n" style="color: #333;">hits</span><span class="p">);</span></span></pre>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="c"><span class="n" style="color: #333;">HashTable</span> <span class="o" style="font-weight: 600;">*</span> <span class="nf" style="color: #900; font-weight: 600;">collect_Kmers</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">HashMapKMA</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">templates</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">Scores</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">long</span></span><span class="idiff right"> </span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">Scores_tot</span><span class="p">,</span> <span class="n" style="color: #333;">HashMap_kmers</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">foundKmers</span><span class="p">,</span> <span class="n" style="color: #333;">Hit</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">hits</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="c"><span class="n" style="color: #333;">HashTable</span> <span class="o" style="font-weight: 600;">**</span> <span class="nf" style="color: #900; font-weight: 600;">collect_Kmers_deCon</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">HashMapKMA</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">templates</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">Scores</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">long</span></span><span class="idiff right"> </span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">Scores_tot</span><span class="p">,</span> <span class="n" style="color: #333;">HashMap_kmers</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">foundKmers</span><span class="p">,</span> <span class="n" style="color: #333;">Hit</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">hits</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">contamination</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="c"><span class="n" style="color: #333;">HashTable</span> <span class="o" style="font-weight: 600;">*</span> <span class="nf" style="color: #900; font-weight: 600;">withDraw_Kmers</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">Scores</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">long</span></span><span class="idiff right"> </span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">Scores_tot</span><span class="p">,</span> <span class="n" style="color: #333;">HashTable</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">kmerList</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">template</span><span class="p">,</span> <span class="n" style="color: #333;">Hit</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">hits</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="c"><span class="n" style="color: #333;">Hit</span> <span class="nf" style="color: #900; font-weight: 600;">withDraw_Contamination</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">Scores</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">long</span></span><span class="idiff right"> </span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">Scores_tot</span><span class="p">,</span> <span class="n" style="color: #333;">HashTable</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">kmerList</span><span class="p">,</span> <span class="n" style="color: #333;">HashTable</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">deConTable</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">template</span><span class="p">,</span> <span class="n" style="color: #333;">Hit</span> <span class="n" style="color: #333;">hits</span><span class="p">);</span></span></pre>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -131,6 +131,7 @@ static void helpMessage(int exeStatus) {</td>
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<pre style="margin: 0;"> <span id="LC131" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">helpOut</span><span class="p">,</span> <span class="s" style="color: #d14;">"#</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">-a</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">Print all best mappings</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">False</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC132" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">helpOut</span><span class="p">,</span> <span class="s" style="color: #d14;">"#</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">-mp</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">Minimum phred score</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">20</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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133
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<td class="diff-line-num new_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">
133
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<pre style="margin: 0;"> <span id="LC133" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">helpOut</span><span class="p">,</span> <span class="s" style="color: #d14;">"#</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">-5p</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">Cut a constant number of</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">#</span><span class="se" style="color: #d14;">\t\t\t</span><span class="s" style="color: #d14;">nucleotides from the 5 prime.</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">0</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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<td class="diff-line-num new old_line" data-linenumber="134" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="134" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">helpOut</span><span class="p">,</span> <span class="s" style="color: #d14;">"#</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">-3p</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">Cut a constant number of</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">#</span><span class="se" style="color: #d14;">\t\t\t</span><span class="s" style="color: #d14;">nucleotides from the 3 prime.</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">0</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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134
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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="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">helpOut</span><span class="p">,</span> <span class="s" style="color: #d14;">"#</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">-Sparse</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">Only count kmers</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">False</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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135
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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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<pre style="margin: 0;"> <span id="LC136" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">helpOut</span><span class="p">,</span> <span class="s" style="color: #d14;">"#</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">-Mt1</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">Map only to </span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">num</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;"> template.</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">0 / False</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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136
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<td class="diff-line-num new_line" data-linenumber="137" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
137
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<pre style="margin: 0;"> <span id="LC137" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">helpOut</span><span class="p">,</span> <span class="s" style="color: #d14;">"#</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">-ID</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">Minimum ID</span><span class="se" style="color: #d14;">\t\t\t</span><span class="s" style="color: #d14;">1.0%%</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="174" style="width: 35px; color: rgba(0,0,0,0.3); 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="175" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -174,11 +175,12 @@ static void helpMessage(int exeStatus) {</td>
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174
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175
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<pre style="margin: 0;"> <span id="LC175" class="line" lang="c"></span>
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175
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176
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<pre style="margin: 0;"> <span id="LC176" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">kma_main</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">argc</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">argv</span><span class="p">[])</span> <span class="p">{</span></span>
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176
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177
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<pre style="margin: 0;"> <span id="LC177" class="line" lang="c"> </span>
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<td class="diff-line-num old old_line" data-linenumber="177" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
177
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<td class="diff-line-num new_line old" data-linenumber="178" style="width: 35px; color: rgba(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="LC177" class="line" lang="c"> <span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">minPhred</span><span class="p">,</span> <span class="n" style="color: #333;">fiveClip</span><span class="p">,</span> <span class="n" style="color: #333;">sparse_run</span><span class="p">,</span> <span class="n" style="color: #333;">mem_mode</span><span class="p">,</span> <span class="n" style="color: #333;">Mt1</span><span class="p">,</span> <span class="n" style="color: #333;">ConClave</span><span class="p">,</span> <span class="n" style="color: #333;">bcd</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="178" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
178
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<td class="diff-line-num new_line old" data-linenumber="178" style="width: 35px; color: rgba(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="LC178" class="line" lang="c"> <span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">fileCounter</span><span class="p">,</span> <span class="n" style="color: #333;">fileCounter_PE</span><span class="p">,</span> <span class="n" style="color: #333;">fileCounter_INT</span><span class="p">,</span> <span class="n" style="color: #333;">targetNum</span><span class="p">,</span> <span class="n" style="color: #333;">vcf</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="179" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
179
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<td class="diff-line-num new_line old" data-linenumber="178" style="width: 35px; color: rgba(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="LC179" class="line" lang="c"> <span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">extendedFeatures</span><span class="p">,</span> <span class="n" style="color: #333;">spltDB</span><span class="p">,</span> <span class="n" style="color: #333;">mq</span><span class="p">,</span> <span class="n" style="color: #333;">thread_num</span><span class="p">,</span> <span class="n" style="color: #333;">kmersize</span><span class="p">,</span> <span class="n" style="color: #333;">one2one</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="180" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
180
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<td class="diff-line-num new_line old" data-linenumber="178" style="width: 35px; color: rgba(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="LC180" class="line" lang="c"> <span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ref_fsa</span><span class="p">,</span> <span class="n" style="color: #333;">print_matrix</span><span class="p">,</span> <span class="n" style="color: #333;">print_all</span><span class="p">,</span> <span class="n" style="color: #333;">sam</span><span class="p">,</span> <span class="n" style="color: #333;">Ts</span><span class="p">,</span> <span class="n" style="color: #333;">Tv</span><span class="p">,</span> <span class="n" style="color: #333;">minlen</span><span class="p">,</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">d</span><span class="p">;</span></span>
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181
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<pre style="margin: 0;">-<span id="LC181" class="line" lang="c"> <span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">nc</span><span class="p">,</span> <span class="n" style="color: #333;">nf</span><span class="p">,</span> <span class="n" style="color: #333;">shm</span><span class="p">,</span> <span class="n" style="color: #333;">exhaustive</span><span class="p">;</span></span>
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178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="c"> <span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">minPhred</span><span class="p">,</span> <span class="n" style="color: #333;">fiveClip</span><span class="p">,</span> <span class="n" style="color: #333;">threeClip</span><span class="p">,</span> <span class="n" style="color: #333;">ConClave</span><span class="p">,</span> <span class="n" style="color: #333;">mem_mode</span><span class="p">,</span> <span class="n" style="color: #333;">sparse_run</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="179" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="c"> <span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">fileCounter</span><span class="p">,</span> <span class="n" style="color: #333;">fileCounter_PE</span><span class="p">,</span> <span class="n" style="color: #333;">fileCounter_INT</span><span class="p">,</span> <span class="n" style="color: #333;">Ts</span><span class="p">,</span> <span class="n" style="color: #333;">Tv</span><span class="p">,</span> <span class="n" style="color: #333;">minlen</span><span class="p">;</span></span>
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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="c"> <span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">extendedFeatures</span><span class="p">,</span> <span class="n" style="color: #333;">spltDB</span><span class="p">,</span> <span class="n" style="color: #333;">thread_num</span><span class="p">,</span> <span class="n" style="color: #333;">kmersize</span><span class="p">,</span> <span class="n" style="color: #333;">targetNum</span><span class="p">,</span> <span class="n" style="color: #333;">mq</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="181" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="c"> <span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ref_fsa</span><span class="p">,</span> <span class="n" style="color: #333;">print_matrix</span><span class="p">,</span> <span class="n" style="color: #333;">print_all</span><span class="p">,</span> <span class="n" style="color: #333;">sam</span><span class="p">,</span> <span class="n" style="color: #333;">vcf</span><span class="p">,</span> <span class="n" style="color: #333;">Mt1</span><span class="p">,</span> <span class="n" style="color: #333;">bcd</span><span class="p">,</span> <span class="n" style="color: #333;">one2one</span><span class="p">;</span></span>
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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="c"> <span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">d</span><span class="p">;</span></span>
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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="c"> <span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">nc</span><span class="p">,</span> <span class="n" style="color: #333;">nf</span><span class="p">,</span> <span class="n" style="color: #333;">shm</span><span class="p">,</span> <span class="n" style="color: #333;">exhaustive</span><span class="p">,</span> <span class="n" style="color: #333;">verbose</span><span class="p">;</span></span>
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182
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<td class="diff-line-num new_line" data-linenumber="184" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
184
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<pre style="margin: 0;"> <span id="LC184" class="line" lang="c"> <span class="k" style="font-weight: 600;">static</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;">outputfilename</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">templatefilename</span><span class="p">,</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">templatefilenames</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="183" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
183
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<td class="diff-line-num new_line" data-linenumber="185" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
185
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<pre style="margin: 0;"> <span id="LC185" class="line" lang="c"> <span class="k" style="font-weight: 600;">static</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;">inputfiles</span><span class="p">,</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">inputfiles_PE</span><span class="p">,</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">inputfiles_INT</span><span class="p">,</span> <span class="n" style="color: #333;">ss</span><span class="p">;</span></span>
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184
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186
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<pre style="margin: 0;"> <span id="LC186" class="line" lang="c"> <span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">ID_t</span><span class="p">,</span> <span class="n" style="color: #333;">scoreT</span><span class="p">,</span> <span class="n" style="color: #333;">coverT</span><span class="p">,</span> <span class="n" style="color: #333;">evalue</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="203" style="width: 35px; color: rgba(0,0,0,0.3); 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="205" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -203,6 +205,7 @@ int kma_main(int argc, char *argv[]) {</td>
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203
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205
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<pre style="margin: 0;"> <span id="LC205" class="line" lang="c"> </span>
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204
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206
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<pre style="margin: 0;"> <span id="LC206" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* SET DEFAULTS */</span></span>
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205
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<td class="diff-line-num 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">
207
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<pre style="margin: 0;"> <span id="LC207" class="line" lang="c"> <span class="n" style="color: #333;">ConClave</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="208" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
208
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="c"> <span class="n" style="color: #333;">verbose</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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206
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<td class="diff-line-num new_line" data-linenumber="209" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
209
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<pre style="margin: 0;"> <span id="LC209" class="line" lang="c"> <span class="n" style="color: #333;">vcf</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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207
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210
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<pre style="margin: 0;"> <span id="LC210" class="line" lang="c"> <span class="n" style="color: #333;">sam</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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208
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211
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<pre style="margin: 0;"> <span id="LC211" class="line" lang="c"> <span class="n" style="color: #333;">nc</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="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">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="216" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -213,6 +216,7 @@ int kma_main(int argc, char *argv[]) {</td>
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213
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216
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<pre style="margin: 0;"> <span id="LC216" class="line" lang="c"> <span class="n" style="color: #333;">status</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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214
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217
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<pre style="margin: 0;"> <span id="LC217" class="line" lang="c"> <span class="n" style="color: #333;">minPhred</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">20</span><span class="p">;</span></span>
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215
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218
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<pre style="margin: 0;"> <span id="LC218" class="line" lang="c"> <span class="n" style="color: #333;">fiveClip</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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219
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="c"> <span class="n" style="color: #333;">threeClip</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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216
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220
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<pre style="margin: 0;"> <span id="LC220" class="line" lang="c"> <span class="n" style="color: #333;">sparse_run</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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217
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221
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<pre style="margin: 0;"> <span id="LC221" class="line" lang="c"> <span class="n" style="color: #333;">fileCounter</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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218
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222
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<pre style="margin: 0;"> <span id="LC222" class="line" lang="c"> <span class="n" style="color: #333;">fileCounter_PE</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="508" style="width: 35px; color: rgba(0,0,0,0.3); 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="512" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -508,6 +512,15 @@ int kma_main(int argc, char *argv[]) {</td>
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508
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512
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<pre style="margin: 0;"> <span id="LC512" class="line" lang="c"> <span class="n" style="color: #333;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">4</span><span class="p">);</span></span>
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509
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513
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<pre style="margin: 0;"> <span id="LC513" class="line" lang="c"> <span class="p">}</span></span>
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510
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514
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<pre style="margin: 0;"> <span id="LC514" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="515" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
515
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<pre style="margin: 0;">+<span id="LC515" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">strcmp</span><span class="p">(</span><span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="n" style="color: #333;">args</span><span class="p">],</span> <span class="s" style="color: #d14;">"-3p"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="516" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
516
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<pre style="margin: 0;">+<span id="LC516" class="line" lang="c"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">args</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="517" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
517
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<pre style="margin: 0;">+<span id="LC517" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">args</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">argc</span><span class="p">)</span> <span class="p">{</span></span>
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518
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<pre style="margin: 0;">+<span id="LC518" class="line" lang="c"> <span class="n" style="color: #333;">threeClip</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">strtoul</span><span class="p">(</span><span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="n" style="color: #333;">args</span><span class="p">],</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">exeBasic</span><span class="p">,</span> <span class="mi" style="color: #099;">10</span><span class="p">);</span></span>
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519
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<pre style="margin: 0;">+<span id="LC519" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">exeBasic</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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520
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<pre style="margin: 0;">+<span id="LC520" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"Invalid argument at </span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">-3p</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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521
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<pre style="margin: 0;">+<span id="LC521" class="line" lang="c"> <span class="n" style="color: #333;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">4</span><span class="p">);</span></span>
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522
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<pre style="margin: 0;">+<span id="LC522" class="line" lang="c"> <span class="p">}</span></span>
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523
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<pre style="margin: 0;">+<span id="LC523" class="line" lang="c"> <span class="p">}</span></span>
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511
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<td class="diff-line-num new_line" data-linenumber="524" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
524
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<pre style="margin: 0;"> <span id="LC524" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">strcmp</span><span class="p">(</span><span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="n" style="color: #333;">args</span><span class="p">],</span> <span class="s" style="color: #d14;">"-dense"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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512
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525
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<pre style="margin: 0;"> <span id="LC525" class="line" lang="c"> <span class="n" style="color: #333;">assembly_KMA_Ptr</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">assemble_KMA_dense_threaded</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="513" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
513
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526
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<pre style="margin: 0;"> <span id="LC526" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">strcmp</span><span class="p">(</span><span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="n" style="color: #333;">args</span><span class="p">],</span> <span class="s" style="color: #d14;">"-sasm"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="798" style="width: 35px; color: rgba(0,0,0,0.3); 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="811" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -798,6 +811,8 @@ int kma_main(int argc, char *argv[]) {</td>
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798
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811
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<pre style="margin: 0;"> <span id="LC811" class="line" lang="c"> <span class="n" style="color: #333;">spltDB</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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799
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<td class="diff-line-num new_line" data-linenumber="812" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
812
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<pre style="margin: 0;"> <span id="LC812" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">strcmp</span><span class="p">(</span><span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="n" style="color: #333;">args</span><span class="p">],</span> <span class="s" style="color: #d14;">"-status"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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800
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<td class="diff-line-num new_line" data-linenumber="813" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
813
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<pre style="margin: 0;"> <span id="LC813" class="line" lang="c"> <span class="n" style="color: #333;">kmaPipe</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">kmaPipeFork</span><span class="p">;</span></span>
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<td class="diff-line-num new old_line" data-linenumber="801" style="width: 35px; color: rgba(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="814" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
814
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<pre style="margin: 0;">+<span id="LC814" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">strcmp</span><span class="p">(</span><span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="n" style="color: #333;">args</span><span class="p">],</span> <span class="s" style="color: #d14;">"-verbose"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new old_line" data-linenumber="801" style="width: 35px; color: rgba(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="815" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
815
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<pre style="margin: 0;">+<span id="LC815" class="line" lang="c"> <span class="n" style="color: #333;">verbose</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="801" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
801
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<td class="diff-line-num new_line" data-linenumber="816" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
816
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<pre style="margin: 0;"> <span id="LC816" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">strcmp</span><span class="p">(</span><span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="n" style="color: #333;">args</span><span class="p">],</span> <span class="s" style="color: #d14;">"-v"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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802
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<td class="diff-line-num new_line" data-linenumber="817" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
817
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<pre style="margin: 0;"> <span id="LC817" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stdout</span><span class="p">,</span> <span class="s" style="color: #d14;">"KMA-%s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">KMA_VERSION</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="803" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
803
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<td class="diff-line-num new_line" data-linenumber="818" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
818
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<pre style="margin: 0;"> <span id="LC818" class="line" lang="c"> <span class="n" style="color: #333;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1079" style="width: 35px; color: rgba(0,0,0,0.3); 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="1094" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -1079,7 +1094,7 @@ int kma_main(int argc, char *argv[]) {</td>
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1079
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<td class="diff-line-num new_line" data-linenumber="1094" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1094
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<pre style="margin: 0;"> <span id="LC1094" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"Interleaved information is not considered in Sparse mode.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="1080" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1080
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<td class="diff-line-num new_line" data-linenumber="1095" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1095
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<pre style="margin: 0;"> <span id="LC1095" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="1081" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1081
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<td class="diff-line-num new_line" data-linenumber="1096" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1096
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<pre style="margin: 0;"> <span id="LC1096" class="line" lang="c"> </span>
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<td class="diff-line-num old old_line" data-linenumber="1082" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1082
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<td class="diff-line-num new_line old" data-linenumber="1097" style="width: 35px; color: rgba(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="LC1082" class="line" lang="c"> <span class="n" style="color: #333;">run_input_sparse</span><span class="p">(</span><span class="n" style="color: #333;">templates</span><span class="p">,</span> <span class="n" style="color: #333;">inputfiles</span><span class="p">,</span> <span class="n" style="color: #333;">fileCounter</span><span class="p">,</span> <span class="n" style="color: #333;">minPhred</span><span class="p">,</span> <span class="n" style="color: #333;">fiveClip</span><span class="p">,</span> <span class="n" style="color: #333;">kmersize</span><span class="p">,</span> <span class="n" style="color: #333;">to2Bit</span><span class="p">,</span> <span class="n" style="color: #333;">ioStream</span><span class="p">);</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1083" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1097" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1097
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<pre style="margin: 0;">+<span id="LC1097" class="line" lang="c"> <span class="n" style="color: #333;">run_input_sparse</span><span class="p">(</span><span class="n" style="color: #333;">templates</span><span class="p">,</span> <span class="n" style="color: #333;">inputfiles</span><span class="p">,</span> <span class="n" style="color: #333;">fileCounter</span><span class="p">,</span> <span class="n" style="color: #333;">minPhred</span><span class="p">,</span> <span class="n" style="color: #333;">fiveClip</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">threeClip</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">kmersize</span><span class="p">,</span> <span class="n" style="color: #333;">to2Bit</span><span class="p">,</span> <span class="n" style="color: #333;">ioStream</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="1083" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1083
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<td class="diff-line-num new_line" data-linenumber="1098" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1098
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<pre style="margin: 0;"> <span id="LC1098" class="line" lang="c"> <span class="n" style="color: #333;">hashMapKMA_destroy</span><span class="p">(</span><span class="n" style="color: #333;">templates</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="1084" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1084
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<td class="diff-line-num new_line" data-linenumber="1099" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1099
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<pre style="margin: 0;"> <span id="LC1099" class="line" lang="c"> <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">myTemplatefilename</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="1085" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1085
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<td class="diff-line-num new_line" data-linenumber="1100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1100
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<pre style="margin: 0;"> <span id="LC1100" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1116" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1101,17 +1116,17 @@ int kma_main(int argc, char *argv[]) {</td>
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1101
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1116
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<pre style="margin: 0;"> <span id="LC1116" class="line" lang="c"> </span>
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<td class="diff-line-num old_line" data-linenumber="1102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1102
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<td class="diff-line-num new_line" data-linenumber="1117" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1117
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<pre style="margin: 0;"> <span id="LC1117" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* SE */</span></span>
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<td class="diff-line-num old_line" data-linenumber="1103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1103
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<td class="diff-line-num new_line" data-linenumber="1118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1118
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<pre style="margin: 0;"> <span id="LC1118" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">fileCounter</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="1104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1104
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<td class="diff-line-num new_line old" data-linenumber="1119" style="width: 35px; color: rgba(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="LC1104" class="line" lang="c"> <span class="n" style="color: #333;">totFrags</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">run_input</span><span class="p">(</span><span class="n" style="color: #333;">inputfiles</span><span class="p">,</span> <span class="n" style="color: #333;">fileCounter</span><span class="p">,</span> <span class="n" style="color: #333;">minPhred</span><span class="p">,</span> <span class="n" style="color: #333;">fiveClip</span><span class="p">,</span> <span class="n" style="color: #333;">minlen</span><span class="p">,</span> <span class="n" style="color: #333;">to2Bit</span><span class="p">,</span> <span class="n" style="color: #333;">ioStream</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1119
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<pre style="margin: 0;">+<span id="LC1119" class="line" lang="c"> <span class="n" style="color: #333;">totFrags</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">run_input</span><span class="p">(</span><span class="n" style="color: #333;">inputfiles</span><span class="p">,</span> <span class="n" style="color: #333;">fileCounter</span><span class="p">,</span> <span class="n" style="color: #333;">minPhred</span><span class="p">,</span> <span class="n" style="color: #333;">fiveClip</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">threeClip</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">minlen</span><span class="p">,</span> <span class="n" style="color: #333;">to2Bit</span><span class="p">,</span> <span class="n" style="color: #333;">ioStream</span><span class="p">);</span></span>
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1105
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<td class="diff-line-num new_line" data-linenumber="1120" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1120
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<pre style="margin: 0;"> <span id="LC1120" class="line" lang="c"> <span class="p">}</span></span>
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1106
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1121
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<pre style="margin: 0;"> <span id="LC1121" class="line" lang="c"> </span>
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<td class="diff-line-num old_line" data-linenumber="1107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1107
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<td class="diff-line-num new_line" data-linenumber="1122" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1122
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<pre style="margin: 0;"> <span id="LC1122" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* PE */</span></span>
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<td class="diff-line-num old_line" data-linenumber="1108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1108
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<td class="diff-line-num new_line" data-linenumber="1123" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1123
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<pre style="margin: 0;"> <span id="LC1123" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">fileCounter_PE</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1109
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<td class="diff-line-num new_line old" data-linenumber="1124" style="width: 35px; color: rgba(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="LC1109" class="line" lang="c"> <span class="n" style="color: #333;">totFrags</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">run_input_PE</span><span class="p">(</span><span class="n" style="color: #333;">inputfiles_PE</span><span class="p">,</span> <span class="n" style="color: #333;">fileCounter_PE</span><span class="p">,</span> <span class="n" style="color: #333;">minPhred</span><span class="p">,</span> <span class="n" style="color: #333;">fiveClip</span><span class="p">,</span> <span class="n" style="color: #333;">minlen</span><span class="p">,</span> <span class="n" style="color: #333;">to2Bit</span><span class="p">,</span> <span class="n" style="color: #333;">ioStream</span><span class="p">);</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1110" style="width: 35px; color: rgba(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="1124" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1124
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<pre style="margin: 0;">+<span id="LC1124" class="line" lang="c"> <span class="n" style="color: #333;">totFrags</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">run_input_PE</span><span class="p">(</span><span class="n" style="color: #333;">inputfiles_PE</span><span class="p">,</span> <span class="n" style="color: #333;">fileCounter_PE</span><span class="p">,</span> <span class="n" style="color: #333;">minPhred</span><span class="p">,</span> <span class="n" style="color: #333;">fiveClip</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">threeClip</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">minlen</span><span class="p">,</span> <span class="n" style="color: #333;">to2Bit</span><span class="p">,</span> <span class="n" style="color: #333;">ioStream</span><span class="p">);</span></span>
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1110
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<td class="diff-line-num new_line" data-linenumber="1125" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1125
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<pre style="margin: 0;"> <span id="LC1125" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="1111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1111
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1126
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<pre style="margin: 0;"> <span id="LC1126" class="line" lang="c"> </span>
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<td class="diff-line-num old_line" data-linenumber="1112" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1112
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<td class="diff-line-num new_line" data-linenumber="1127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1127
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<pre style="margin: 0;"> <span id="LC1127" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* INT */</span></span>
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<td class="diff-line-num old_line" data-linenumber="1113" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1113
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<td class="diff-line-num new_line" data-linenumber="1128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1128
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<pre style="margin: 0;"> <span id="LC1128" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">fileCounter_INT</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1114" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1114
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<td class="diff-line-num new_line old" data-linenumber="1129" style="width: 35px; color: rgba(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="LC1114" class="line" lang="c"> <span class="n" style="color: #333;">totFrags</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">run_input_INT</span><span class="p">(</span><span class="n" style="color: #333;">inputfiles_INT</span><span class="p">,</span> <span class="n" style="color: #333;">fileCounter_INT</span><span class="p">,</span> <span class="n" style="color: #333;">minPhred</span><span class="p">,</span> <span class="n" style="color: #333;">fiveClip</span><span class="p">,</span> <span class="n" style="color: #333;">minlen</span><span class="p">,</span> <span class="n" style="color: #333;">to2Bit</span><span class="p">,</span> <span class="n" style="color: #333;">ioStream</span><span class="p">);</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1115" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1129
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<pre style="margin: 0;">+<span id="LC1129" class="line" lang="c"> <span class="n" style="color: #333;">totFrags</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">run_input_INT</span><span class="p">(</span><span class="n" style="color: #333;">inputfiles_INT</span><span class="p">,</span> <span class="n" style="color: #333;">fileCounter_INT</span><span class="p">,</span> <span class="n" style="color: #333;">minPhred</span><span class="p">,</span> <span class="n" style="color: #333;">fiveClip</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">threeClip</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">minlen</span><span class="p">,</span> <span class="n" style="color: #333;">to2Bit</span><span class="p">,</span> <span class="n" style="color: #333;">ioStream</span><span class="p">);</span></span>
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1115
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<td class="diff-line-num new_line" data-linenumber="1130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1130
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<pre style="margin: 0;"> <span id="LC1130" class="line" lang="c"> <span class="p">}</span></span>
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1116
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1131
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<pre style="margin: 0;"> <span id="LC1131" class="line" lang="c"> </span>
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<td class="diff-line-num old_line" data-linenumber="1117" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1117
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<td class="diff-line-num new_line" data-linenumber="1132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1132
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<pre style="margin: 0;"> <span id="LC1132" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">Mt1</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1149" style="width: 35px; color: rgba(0,0,0,0.3); 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="1164" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -1149,11 +1164,11 @@ int kma_main(int argc, char *argv[]) {</td>
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1149
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<td class="diff-line-num new_line" data-linenumber="1164" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1164
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<pre style="margin: 0;"> <span id="LC1164" class="line" lang="c"> <span class="n" style="color: #333;">myTemplatefilename</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">smalloc</span><span class="p">(</span><span class="n" style="color: #333;">strlen</span><span class="p">(</span><span class="n" style="color: #333;">templatefilename</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">64</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="1150" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1150
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<td class="diff-line-num new_line" data-linenumber="1165" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1165
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<pre style="margin: 0;"> <span id="LC1165" class="line" lang="c"> <span class="n" style="color: #333;">strcpy</span><span class="p">(</span><span class="n" style="color: #333;">myTemplatefilename</span><span class="p">,</span> <span class="n" style="color: #333;">templatefilename</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="1151" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1151
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<td class="diff-line-num new_line" data-linenumber="1166" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1166
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<pre style="margin: 0;"> <span id="LC1166" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">spltDB</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">targetNum</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1152" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1152
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<td class="diff-line-num new_line old" data-linenumber="1167" style="width: 35px; color: rgba(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="LC1152" class="line" lang="c"> <span class="n" style="color: #333;">status</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">runKMA_spltDB</span><span class="p">(</span><span class="n" style="color: #333;">templatefilenames</span><span class="p">,</span> <span class="n" style="color: #333;">targetNum</span><span class="p">,</span> <span class="n" style="color: #333;">outputfilename</span><span class="p">,</span> <span class="n" style="color: #333;">argc</span><span class="p">,</span> <span class="n" style="color: #333;">argv</span><span class="p">,</span> <span class="n" style="color: #333;">ConClave</span><span class="p">,</span> <span class="n" style="color: #333;">kmersize</span><span class="p">,</span> <span class="n" style="color: #333;">minlen</span><span class="p">,</span> <span class="n" style="color: #333;">rewards</span><span class="p">,</span> <span class="n" style="color: #333;">extendedFeatures</span><span class="p">,</span> <span class="n" style="color: #333;">ID_t</span><span class="p">,</span> <span class="n" style="color: #333;">mq</span><span class="p">,</span> <span class="n" style="color: #333;">scoreT</span><span class="p">,</span> <span class="n" style="color: #333;">evalue</span><span class="p">,</span> <span class="n" style="color: #333;">bcd</span><span class="p">,</span> <span class="n" style="color: #333;">ref_fsa</span><span class="p">,</span> <span class="n" style="color: #333;">print_matrix</span><span class="p">,</span> <span class="n" style="color: #333;">print_all</span><span class="p">,</span> <span class="n" style="color: #333;">vcf</span><span class="p">,</span> <span class="n" style="color: #333;">sam</span><span class="p">,</span> <span class="n" style="color: #333;">nc</span><span class="p">,</span> <span class="n" style="color: #333;">nf</span><span class="p">,</span> <span class="n" style="color: #333;">shm</span><span class="p">,</span> <span class="n" style="color: #333;">thread_num</span><span class="p">);</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1153" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1167" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1167
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<pre style="margin: 0;">+<span id="LC1167" class="line" lang="c"> <span class="n" style="color: #333;">status</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">runKMA_spltDB</span><span class="p">(</span><span class="n" style="color: #333;">templatefilenames</span><span class="p">,</span> <span class="n" style="color: #333;">targetNum</span><span class="p">,</span> <span class="n" style="color: #333;">outputfilename</span><span class="p">,</span> <span class="n" style="color: #333;">argc</span><span class="p">,</span> <span class="n" style="color: #333;">argv</span><span class="p">,</span> <span class="n" style="color: #333;">ConClave</span><span class="p">,</span> <span class="n" style="color: #333;">kmersize</span><span class="p">,</span> <span class="n" style="color: #333;">minlen</span><span class="p">,</span> <span class="n" style="color: #333;">rewards</span><span class="p">,</span> <span class="n" style="color: #333;">extendedFeatures</span><span class="p">,</span> <span class="n" style="color: #333;">ID_t</span><span class="p">,</span> <span class="n" style="color: #333;">mq</span><span class="p">,</span> <span class="n" style="color: #333;">scoreT</span><span class="p">,</span> <span class="n" style="color: #333;">evalue</span><span class="p">,</span> <span class="n" style="color: #333;">bcd</span><span class="p">,</span> <span class="n" style="color: #333;">ref_fsa</span><span class="p">,</span> <span class="n" style="color: #333;">print_matrix</span><span class="p">,</span> <span class="n" style="color: #333;">print_all</span><span class="p">,</span> <span class="n" style="color: #333;">vcf</span><span class="p">,</span> <span class="n" style="color: #333;">sam</span><span class="p">,</span> <span class="n" style="color: #333;">nc</span><span class="p">,</span> <span class="n" style="color: #333;">nf</span><span class="p">,</span> <span class="n" style="color: #333;">shm</span><span class="p">,</span> <span class="n" style="color: #333;">thread_num</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">verbose</span></span><span class="p">);</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1153" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1153
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<td class="diff-line-num new_line" data-linenumber="1168" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1168
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<pre style="margin: 0;"> <span id="LC1168" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">mem_mode</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1154" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1154
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<td class="diff-line-num new_line old" data-linenumber="1169" style="width: 35px; color: rgba(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="LC1154" class="line" lang="c"> <span class="n" style="color: #333;">status</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">runKMA_MEM</span><span class="p">(</span><span class="n" style="color: #333;">myTemplatefilename</span><span class="p">,</span> <span class="n" style="color: #333;">outputfilename</span><span class="p">,</span> <span class="n" style="color: #333;">exeBasic</span><span class="p">,</span> <span class="n" style="color: #333;">ConClave</span><span class="p">,</span> <span class="n" style="color: #333;">kmersize</span><span class="p">,</span> <span class="n" style="color: #333;">minlen</span><span class="p">,</span> <span class="n" style="color: #333;">rewards</span><span class="p">,</span> <span class="n" style="color: #333;">extendedFeatures</span><span class="p">,</span> <span class="n" style="color: #333;">ID_t</span><span class="p">,</span> <span class="n" style="color: #333;">mq</span><span class="p">,</span> <span class="n" style="color: #333;">scoreT</span><span class="p">,</span> <span class="n" style="color: #333;">evalue</span><span class="p">,</span> <span class="n" style="color: #333;">bcd</span><span class="p">,</span> <span class="n" style="color: #333;">ref_fsa</span><span class="p">,</span> <span class="n" style="color: #333;">print_matrix</span><span class="p">,</span> <span class="n" style="color: #333;">print_all</span><span class="p">,</span> <span class="n" style="color: #333;">vcf</span><span class="p">,</span> <span class="n" style="color: #333;">sam</span><span class="p">,</span> <span class="n" style="color: #333;">nc</span><span class="p">,</span> <span class="n" style="color: #333;">nf</span><span class="p">,</span> <span class="n" style="color: #333;">shm</span><span class="p">,</span> <span class="n" style="color: #333;">thread_num</span><span class="p">);</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1155" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1169" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1169
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1169" class="line" lang="c"> <span class="n" style="color: #333;">status</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">runKMA_MEM</span><span class="p">(</span><span class="n" style="color: #333;">myTemplatefilename</span><span class="p">,</span> <span class="n" style="color: #333;">outputfilename</span><span class="p">,</span> <span class="n" style="color: #333;">exeBasic</span><span class="p">,</span> <span class="n" style="color: #333;">ConClave</span><span class="p">,</span> <span class="n" style="color: #333;">kmersize</span><span class="p">,</span> <span class="n" style="color: #333;">minlen</span><span class="p">,</span> <span class="n" style="color: #333;">rewards</span><span class="p">,</span> <span class="n" style="color: #333;">extendedFeatures</span><span class="p">,</span> <span class="n" style="color: #333;">ID_t</span><span class="p">,</span> <span class="n" style="color: #333;">mq</span><span class="p">,</span> <span class="n" style="color: #333;">scoreT</span><span class="p">,</span> <span class="n" style="color: #333;">evalue</span><span class="p">,</span> <span class="n" style="color: #333;">bcd</span><span class="p">,</span> <span class="n" style="color: #333;">ref_fsa</span><span class="p">,</span> <span class="n" style="color: #333;">print_matrix</span><span class="p">,</span> <span class="n" style="color: #333;">print_all</span><span class="p">,</span> <span class="n" style="color: #333;">vcf</span><span class="p">,</span> <span class="n" style="color: #333;">sam</span><span class="p">,</span> <span class="n" style="color: #333;">nc</span><span class="p">,</span> <span class="n" style="color: #333;">nf</span><span class="p">,</span> <span class="n" style="color: #333;">shm</span><span class="p">,</span> <span class="n" style="color: #333;">thread_num</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">verbose</span></span><span class="p">);</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1155" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1155
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<td class="diff-line-num new_line" data-linenumber="1170" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1170
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<pre style="margin: 0;"> <span id="LC1170" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="1156" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1156
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<td class="diff-line-num new_line old" data-linenumber="1171" style="width: 35px; color: rgba(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="LC1156" class="line" lang="c"> <span class="n" style="color: #333;">status</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">runKMA</span><span class="p">(</span><span class="n" style="color: #333;">myTemplatefilename</span><span class="p">,</span> <span class="n" style="color: #333;">outputfilename</span><span class="p">,</span> <span class="n" style="color: #333;">exeBasic</span><span class="p">,</span> <span class="n" style="color: #333;">ConClave</span><span class="p">,</span> <span class="n" style="color: #333;">kmersize</span><span class="p">,</span> <span class="n" style="color: #333;">minlen</span><span class="p">,</span> <span class="n" style="color: #333;">rewards</span><span class="p">,</span> <span class="n" style="color: #333;">extendedFeatures</span><span class="p">,</span> <span class="n" style="color: #333;">ID_t</span><span class="p">,</span> <span class="n" style="color: #333;">mq</span><span class="p">,</span> <span class="n" style="color: #333;">scoreT</span><span class="p">,</span> <span class="n" style="color: #333;">evalue</span><span class="p">,</span> <span class="n" style="color: #333;">bcd</span><span class="p">,</span> <span class="n" style="color: #333;">ref_fsa</span><span class="p">,</span> <span class="n" style="color: #333;">print_matrix</span><span class="p">,</span> <span class="n" style="color: #333;">print_all</span><span class="p">,</span> <span class="n" style="color: #333;">vcf</span><span class="p">,</span> <span class="n" style="color: #333;">sam</span><span class="p">,</span> <span class="n" style="color: #333;">nc</span><span class="p">,</span> <span class="n" style="color: #333;">nf</span><span class="p">,</span> <span class="n" style="color: #333;">shm</span><span class="p">,</span> <span class="n" style="color: #333;">thread_num</span><span class="p">);</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1171" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1171
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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="LC1171" class="line" lang="c"> <span class="n" style="color: #333;">status</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">runKMA</span><span class="p">(</span><span class="n" style="color: #333;">myTemplatefilename</span><span class="p">,</span> <span class="n" style="color: #333;">outputfilename</span><span class="p">,</span> <span class="n" style="color: #333;">exeBasic</span><span class="p">,</span> <span class="n" style="color: #333;">ConClave</span><span class="p">,</span> <span class="n" style="color: #333;">kmersize</span><span class="p">,</span> <span class="n" style="color: #333;">minlen</span><span class="p">,</span> <span class="n" style="color: #333;">rewards</span><span class="p">,</span> <span class="n" style="color: #333;">extendedFeatures</span><span class="p">,</span> <span class="n" style="color: #333;">ID_t</span><span class="p">,</span> <span class="n" style="color: #333;">mq</span><span class="p">,</span> <span class="n" style="color: #333;">scoreT</span><span class="p">,</span> <span class="n" style="color: #333;">evalue</span><span class="p">,</span> <span class="n" style="color: #333;">bcd</span><span class="p">,</span> <span class="n" style="color: #333;">ref_fsa</span><span class="p">,</span> <span class="n" style="color: #333;">print_matrix</span><span class="p">,</span> <span class="n" style="color: #333;">print_all</span><span class="p">,</span> <span class="n" style="color: #333;">vcf</span><span class="p">,</span> <span class="n" style="color: #333;">sam</span><span class="p">,</span> <span class="n" style="color: #333;">nc</span><span class="p">,</span> <span class="n" style="color: #333;">nf</span><span class="p">,</span> <span class="n" style="color: #333;">shm</span><span class="p">,</span> <span class="n" style="color: #333;">thread_num</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">verbose</span></span><span class="p">);</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1157
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<td class="diff-line-num new_line" data-linenumber="1172" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1172
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<pre style="margin: 0;"> <span id="LC1172" class="line" lang="c"> <span class="p">}</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1158" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1158
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<td class="diff-line-num new_line" data-linenumber="1173" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1173
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1173" class="line" lang="c"> <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">myTemplatefilename</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="1159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1159
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<td class="diff-line-num new_line" data-linenumber="1174" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1174
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<pre style="margin: 0;"> <span id="LC1174" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"# Closing files</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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<a href="https://salsa.debian.org/med-team/kma/-/commit/2f19ae42ee0599842c05907229fbcefcd490ae07#24b1ddd54f1e7a0b2170af91261c0ecfa055c98d"><strong>runinput.c</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">@@ -28,7 +28,7 @@</td>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">printFsa_ptr</span><span class="p">)(</span><span class="n" style="color: #333;">Qseqs</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="n" style="color: #333;">Qseqs</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="n" style="color: #333;">CompDNA</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">FILE</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">printFsa</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">printFsa_pair_ptr</span><span class="p">)(</span><span class="n" style="color: #333;">Qseqs</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="n" style="color: #333;">Qseqs</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="n" style="color: #333;">Qseqs</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="n" style="color: #333;">Qseqs</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="n" style="color: #333;">CompDNA</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">FILE</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">printFsa_pair</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="nf" style="color: #900; font-weight: 600;">run_input</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;">inputfiles</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">fileCount</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">minPhred</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">fiveClip</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">minlen</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;">trans</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">out</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="nf" style="color: #900; font-weight: 600;">run_input</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;">inputfiles</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">fileCount</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">minPhred</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">fiveClip</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;"><span class="idiff left">threeClip</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">int</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">minlen</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;">trans</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">out</span><span class="p">)</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="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">fileCounter</span><span class="p">,</span> <span class="n" style="color: #333;">phredCut</span><span class="p">,</span> <span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="n" style="color: #333;">end</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">FASTQ</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">@@ -67,7 +67,8 @@ long unsigned run_input(char **inputfiles, int fileCount, int minPhred, int five</td>
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* trim */</span></span>
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="c"> <span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">qual</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seq</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="c"> <span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fiveClip</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="c"> <span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">qseq</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="c"> <span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">qseq</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">threeClip</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="c"> <span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">?</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">end</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="c"> <span class="k" style="font-weight: 600;">while</span><span class="p">(</span><span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">seq</span><span class="p">[</span><span class="n" style="color: #333;">end</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">phredCut</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="c"> <span class="o" style="font-weight: 600;">--</span><span class="n" style="color: #333;">end</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="c"> <span class="p">}</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -133,7 +134,7 @@ long unsigned run_input(char **inputfiles, int fileCount, int minPhred, int five</td>
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<pre style="margin: 0;"> <span id="LC134" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">count</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC135" class="line" lang="c"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC136" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC136" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="nf" style="color: #900; font-weight: 600;">run_input_PE</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;">inputfiles</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">fileCount</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">minPhred</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">fiveClip</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">minlen</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;">trans</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">out</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="nf" style="color: #900; font-weight: 600;">run_input_PE</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;">inputfiles</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">fileCount</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">minPhred</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">fiveClip</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;"><span class="idiff left">threeClip</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">int</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">minlen</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;">trans</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">out</span><span class="p">)</span> <span class="p">{</span></span>
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138
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<pre style="margin: 0;"> <span id="LC138" class="line" lang="c"> </span>
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138
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139
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<pre style="margin: 0;"> <span id="LC139" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">fileCounter</span><span class="p">,</span> <span class="n" style="color: #333;">phredCut</span><span class="p">,</span> <span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="n" style="color: #333;">start2</span><span class="p">,</span> <span class="n" style="color: #333;">end</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC140" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">FASTQ</span><span class="p">,</span> <span class="n" style="color: #333;">FASTQ2</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="192" style="width: 35px; color: rgba(0,0,0,0.3); 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="193" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -192,7 +193,8 @@ long unsigned run_input_PE(char **inputfiles, int fileCount, int minPhred, int f</td>
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192
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<pre style="margin: 0;"> <span id="LC193" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* trim forward */</span></span>
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193
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<pre style="margin: 0;"> <span id="LC194" class="line" lang="c"> <span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">qual</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seq</span><span class="p">;</span></span>
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194
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<pre style="margin: 0;"> <span id="LC195" class="line" lang="c"> <span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fiveClip</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC195" class="line" lang="c"> <span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">qseq</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="c"> <span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">qseq</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">threeClip</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="c"> <span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">?</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">end</span><span class="p">;</span></span>
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196
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<pre style="margin: 0;"> <span id="LC198" class="line" lang="c"> <span class="k" style="font-weight: 600;">while</span><span class="p">(</span><span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">seq</span><span class="p">[</span><span class="n" style="color: #333;">end</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">phredCut</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC199" class="line" lang="c"> <span class="o" style="font-weight: 600;">--</span><span class="n" style="color: #333;">end</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC200" class="line" lang="c"> <span class="p">}</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -326,7 +328,7 @@ long unsigned run_input_PE(char **inputfiles, int fileCount, int minPhred, int f</td>
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<pre style="margin: 0;"> <span id="LC328" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">count</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC329" class="line" lang="c"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC330" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC329" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="nf" style="color: #900; font-weight: 600;">run_input_INT</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;">inputfiles</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">fileCount</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">minPhred</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">fiveClip</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">minlen</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;">trans</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">out</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC331" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="nf" style="color: #900; font-weight: 600;">run_input_INT</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;">inputfiles</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">fileCount</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">minPhred</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">fiveClip</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;"><span class="idiff left">threeClip</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">int</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">minlen</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;">trans</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">out</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC332" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC333" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">fileCounter</span><span class="p">,</span> <span class="n" style="color: #333;">phredCut</span><span class="p">,</span> <span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="n" style="color: #333;">start2</span><span class="p">,</span> <span class="n" style="color: #333;">end</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC334" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">FASTQ</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="374" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -372,7 +374,8 @@ long unsigned run_input_INT(char **inputfiles, int fileCount, int minPhred, int</td>
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<pre style="margin: 0;"> <span id="LC374" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* trim forward */</span></span>
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<pre style="margin: 0;"> <span id="LC375" class="line" lang="c"> <span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">qual</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seq</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC376" class="line" lang="c"> <span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fiveClip</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC375" class="line" lang="c"> <span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">qseq</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC377" class="line" lang="c"> <span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">qseq</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">threeClip</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC378" class="line" lang="c"> <span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">?</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">end</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC379" class="line" lang="c"> <span class="k" style="font-weight: 600;">while</span><span class="p">(</span><span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">seq</span><span class="p">[</span><span class="n" style="color: #333;">end</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">phredCut</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC380" class="line" lang="c"> <span class="o" style="font-weight: 600;">--</span><span class="n" style="color: #333;">end</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC381" class="line" lang="c"> <span class="p">}</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -23,9 +23,9 @@</td>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/* pointers determining how to deliver the input */</span></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="c"><span class="k" style="font-weight: 600;">extern</span> <span class="nf" style="color: #900; font-weight: 600;">void</span> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">printFsa_ptr</span><span class="p">)(</span><span class="n" style="color: #333;">Qseqs</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="n" style="color: #333;">Qseqs</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="n" style="color: #333;">CompDNA</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">FILE</span><span class="o" style="font-weight: 600;">*</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="c"><span class="k" style="font-weight: 600;">extern</span> <span class="nf" style="color: #900; font-weight: 600;">void</span> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">printFsa_pair_ptr</span><span class="p">)(</span><span class="n" style="color: #333;">Qseqs</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="n" style="color: #333;">Qseqs</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="n" style="color: #333;">Qseqs</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="n" style="color: #333;">Qseqs</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="n" style="color: #333;">CompDNA</span><span class="o" style="font-weight: 600;">*</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">FILE</span><span class="o" style="font-weight: 600;">*</span><span class="p">);</span></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;">long</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="nf" style="color: #900; font-weight: 600;">run_input</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;">inputfiles</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">fileCount</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">minPhred</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">fiveClip</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">minlen</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;">trans</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">out</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="nf" style="color: #900; font-weight: 600;">run_input_PE</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;">inputfiles</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">fileCount</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">minPhred</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">fiveClip</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">minlen</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;">trans</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">out</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="nf" style="color: #900; font-weight: 600;">run_input_INT</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;">inputfiles</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">fileCount</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">minPhred</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">fiveClip</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">minlen</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;">trans</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">out</span><span class="p">);</span></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;">long</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="nf" style="color: #900; font-weight: 600;">run_input</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;">inputfiles</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">fileCount</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">minPhred</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">fiveClip</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;"><span class="idiff left">threeClip</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">int</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">minlen</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;">trans</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">out</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="nf" style="color: #900; font-weight: 600;">run_input_PE</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;">inputfiles</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">fileCount</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">minPhred</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">fiveClip</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;"><span class="idiff left">threeClip</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">int</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">minlen</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;">trans</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">out</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="nf" style="color: #900; font-weight: 600;">run_input_INT</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;">inputfiles</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">fileCount</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">minPhred</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">fiveClip</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;"><span class="idiff left">threeClip</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">int</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">minlen</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;">trans</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">out</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">bootFsa</span><span class="p">(</span><span class="n" style="color: #333;">Qseqs</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">header</span><span class="p">,</span> <span class="n" style="color: #333;">Qseqs</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq</span><span class="p">,</span> <span class="n" style="color: #333;">CompDNA</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">compressor</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">out</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">printFsa</span><span class="p">(</span><span class="n" style="color: #333;">Qseqs</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">header</span><span class="p">,</span> <span class="n" style="color: #333;">Qseqs</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq</span><span class="p">,</span> <span class="n" style="color: #333;">CompDNA</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">compressor</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">out</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">printFsa_pair</span><span class="p">(</span><span class="n" style="color: #333;">Qseqs</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">header</span><span class="p">,</span> <span class="n" style="color: #333;">Qseqs</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq</span><span class="p">,</span> <span class="n" style="color: #333;">Qseqs</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">header_r</span><span class="p">,</span> <span class="n" style="color: #333;">Qseqs</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq_r</span><span class="p">,</span> <span class="n" style="color: #333;">CompDNA</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">compressor</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">out</span><span class="p">);</span></span></pre>
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<a href="https://salsa.debian.org/med-team/kma/-/commit/2f19ae42ee0599842c05907229fbcefcd490ae07#ca9efd475143efe0a1b0464c67f49900d98ca75a"><strong>runkma.c</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">@@ -134,14 +134,14 @@ char * nameLoad(Qseqs *name, FILE *infile) {</td>
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<pre style="margin: 0;"> <span id="LC134" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="p">)</span> <span class="n" style="color: #333;">name</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seq</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC135" class="line" lang="c"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC136" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC137" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">runKMA</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;">templatefilename</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;">outputfilename</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;">exePrev</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ConClave</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">kmersize</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">minlen</span><span class="p">,</span> <span class="n" style="color: #333;">Penalties</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">rewards</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">extendedFeatures</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">ID_t</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">mq</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">scoreT</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">evalue</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">bcd</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ref_fsa</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">print_matrix</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">print_all</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">vcf</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">sam</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nc</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nf</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">shm</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">thread_num</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">runKMA</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;">templatefilename</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;">outputfilename</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;">exePrev</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ConClave</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">kmersize</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">minlen</span><span class="p">,</span> <span class="n" style="color: #333;">Penalties</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">rewards</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">extendedFeatures</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">ID_t</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">mq</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">scoreT</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">evalue</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">bcd</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ref_fsa</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">print_matrix</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">print_all</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">vcf</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">sam</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nc</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nf</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">shm</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">thread_num</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">int</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">verbose</span></span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC138" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC139" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">j</span><span class="p">,</span> <span class="n" style="color: #333;">tmp_template</span><span class="p">,</span> <span class="n" style="color: #333;">tmp_tmp_template</span><span class="p">,</span> <span class="n" style="color: #333;">file_len</span><span class="p">,</span> <span class="n" style="color: #333;">bestTemplate</span><span class="p">,</span> <span class="n" style="color: #333;">tot</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC140" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">template</span><span class="p">,</span> <span class="n" style="color: #333;">bestHits</span><span class="p">,</span> <span class="n" style="color: #333;">t_len</span><span class="p">,</span> <span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="n" style="color: #333;">end</span><span class="p">,</span> <span class="n" style="color: #333;">aln_len</span><span class="p">,</span> <span class="n" style="color: #333;">status</span><span class="p">,</span> <span class="n" style="color: #333;">rand</span><span class="p">,</span> <span class="n" style="color: #333;">sparse</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC141" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">fragCount</span><span class="p">,</span> <span class="n" style="color: #333;">fileCount</span><span class="p">,</span> <span class="n" style="color: #333;">maxFrag</span><span class="p">,</span> <span class="n" style="color: #333;">coverScore</span><span class="p">,</span> <span class="n" style="color: #333;">tmp_start</span><span class="p">,</span> <span class="n" style="color: #333;">tmp_end</span><span class="p">,</span> <span class="n" style="color: #333;">score</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC142" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">index_in_no</span><span class="p">,</span> <span class="n" style="color: #333;">seq_in_no</span><span class="p">,</span> <span class="n" style="color: #333;">DB_size</span><span class="p">,</span> <span class="n" style="color: #333;">flag</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">stats</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">5</span></span><span class="p"><span class="idiff">],</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="n" style="color: #333;"><span class="idiff right">matched_templates</span></span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">index_in_no</span><span class="p">,</span> <span class="n" style="color: #333;">seq_in_no</span><span class="p">,</span> <span class="n" style="color: #333;">DB_size</span><span class="p">,</span> <span class="n" style="color: #333;">flag</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">counter</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">stats</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">5</span></span><span class="p"><span class="idiff right">]</span>;</span></span>
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<pre style="margin: 0;"> <span id="LC143" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">bestTemplates</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">bestTemplates_r</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">best_start_pos</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">best_end_pos</span><span class="p">;</span></span>
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144
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<pre style="margin: 0;">-<span id="LC144" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">template_lengths</span><span class="p">;</span></span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;"><span class="idiff left">matched_templates</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff right">*</span></span><span class="n" style="color: #333;">template_lengths</span><span class="p">;</span></span>
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145
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<pre style="margin: 0;"> <span id="LC145" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">randScore</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fragmentCounts</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">readCounts</span><span class="p">;</span></span>
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146
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146
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<pre style="margin: 0;"> <span id="LC146" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="n" style="color: #333;">read_score</span><span class="p">,</span> <span class="n" style="color: #333;">best_read_score</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">index_indexes</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">seq_indexes</span><span class="p">;</span></span>
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147
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147
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<pre style="margin: 0;"> <span id="LC147" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">Nhits</span><span class="p">,</span> <span class="n" style="color: #333;">template_tot_ulen</span><span class="p">,</span> <span class="n" style="color: #333;">bestNum</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1164" style="width: 35px; color: rgba(0,0,0,0.3); 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="1164" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -1164,14 +1164,22 @@ int runKMA(char *templatefilename, char *outputfilename, char *exePrev, int ConC</td>
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1164
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1164
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<pre style="margin: 0;"> <span id="LC1164" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">assembly_KMA_Ptr</span> <span class="o" style="font-weight: 600;">==</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">skip_assemble_KMA</span><span class="p">)</span> <span class="p">{</span></span>
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1165
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1165
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<pre style="margin: 0;"> <span id="LC1165" class="line" lang="c"> <span class="n" style="color: #333;">alignLoadPtr</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">alignLoad_skip</span><span class="p">;</span></span>
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1166
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1166
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<pre style="margin: 0;"> <span id="LC1166" class="line" lang="c"> <span class="p">}</span></span>
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1167
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<pre style="margin: 0;">+<span id="LC1167" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">verbose</span><span class="p">)</span> <span class="p">{</span></span>
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1168
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<pre style="margin: 0;">+<span id="LC1168" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"# Template</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">Score</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">Progress</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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1169
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<pre style="margin: 0;">+<span id="LC1169" class="line" lang="c"> <span class="p">}</span></span>
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1167
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1170
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<pre style="margin: 0;"> <span id="LC1170" class="line" lang="c"> </span>
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1168
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1171
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<pre style="margin: 0;"> <span id="LC1171" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Do local assemblies of fragments mapping to the same template */</span></span>
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1169
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1172
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<pre style="margin: 0;"> <span id="LC1172" class="line" lang="c"> <span class="n" style="color: #333;">depth</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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1170
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1173
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<pre style="margin: 0;"> <span id="LC1173" class="line" lang="c"> <span class="n" style="color: #333;">q_id</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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1171
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1174
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<pre style="margin: 0;"> <span id="LC1174" class="line" lang="c"> <span class="n" style="color: #333;">cover</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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1172
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1175
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<pre style="margin: 0;"> <span id="LC1175" class="line" lang="c"> <span class="n" style="color: #333;">q_cover</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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1176
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<pre style="margin: 0;">+<span id="LC1176" class="line" lang="c"> <span class="n" style="color: #333;">counter</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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1173
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1177
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<pre style="margin: 0;"> <span id="LC1177" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="n" style="color: #333;">template</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;">template</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">DB_size</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">template</span><span class="p">)</span> <span class="p">{</span></span>
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1174
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<td class="diff-line-num new_line" data-linenumber="1178" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1178
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<pre style="margin: 0;"> <span id="LC1178" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">w_scores</span><span class="p">[</span><span class="n" style="color: #333;">template</span><span class="p">]</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1179" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1179
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<pre style="margin: 0;">+<span id="LC1179" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">verbose</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1180" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1180
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<pre style="margin: 0;">+<span id="LC1180" class="line" lang="c"> <span class="n" style="color: #333;">counter</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">w_scores</span><span class="p">[</span><span class="n" style="color: #333;">template</span><span class="p">];</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1181" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1181
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<pre style="margin: 0;">+<span id="LC1181" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"# %d / %d</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%lu</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%3lu%%</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">template</span><span class="p">,</span> <span class="n" style="color: #333;">DB_size</span><span class="p">,</span> <span class="n" style="color: #333;">w_scores</span><span class="p">[</span><span class="n" style="color: #333;">template</span><span class="p">],</span> <span class="mi" style="color: #099;">100</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">counter</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">Nhits</span><span class="p">);</span></span>
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1182
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<pre style="margin: 0;">+<span id="LC1182" class="line" lang="c"> <span class="p">}</span></span>
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1175
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1183
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<pre style="margin: 0;"> <span id="LC1183" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* make p_value to see whether assembly is feasable */</span></span>
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1176
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1184
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<pre style="margin: 0;"> <span id="LC1184" class="line" lang="c"> <span class="n" style="color: #333;">read_score</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">w_scores</span><span class="p">[</span><span class="n" style="color: #333;">template</span><span class="p">];</span></span>
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<td class="diff-line-num old_line" data-linenumber="1177" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1177
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1185
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<pre style="margin: 0;"> <span id="LC1185" class="line" lang="c"> <span class="n" style="color: #333;">t_len</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">template_lengths</span><span class="p">[</span><span class="n" style="color: #333;">template</span><span class="p">];</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1293" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -1293,7 +1301,7 @@ int runKMA(char *templatefilename, char *outputfilename, char *exePrev, int ConC</td>
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1293
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1301
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<pre style="margin: 0;"> <span id="LC1301" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">status</span><span class="p">;</span></span>
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1294
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1302
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<pre style="margin: 0;"> <span id="LC1302" class="line" lang="c"><span class="p">}</span></span>
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1295
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1303
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<pre style="margin: 0;"> <span id="LC1303" class="line" lang="c"></span>
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1296
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<pre style="margin: 0;">-<span id="LC1296" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">runKMA_MEM</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;">templatefilename</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;">outputfilename</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;">exePrev</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ConClave</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">kmersize</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">minlen</span><span class="p">,</span> <span class="n" style="color: #333;">Penalties</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">rewards</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">extendedFeatures</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">ID_t</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">mq</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">scoreT</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">evalue</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">bcd</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ref_fsa</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">print_matrix</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">print_all</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">vcf</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">sam</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nc</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nf</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">shm</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">thread_num</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC1304" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">runKMA_MEM</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;">templatefilename</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;">outputfilename</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;">exePrev</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ConClave</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">kmersize</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">minlen</span><span class="p">,</span> <span class="n" style="color: #333;">Penalties</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">rewards</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">extendedFeatures</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">ID_t</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">mq</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">scoreT</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">evalue</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">bcd</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ref_fsa</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">print_matrix</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">print_all</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">vcf</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">sam</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nc</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nf</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">shm</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">thread_num</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">int</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">verbose</span></span><span class="p">)</span> <span class="p">{</span></span>
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1297
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1305
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<pre style="margin: 0;"> <span id="LC1305" class="line" lang="c"> </span>
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1298
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1306
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<pre style="margin: 0;"> <span id="LC1306" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* runKMA_MEM is a memory saving version of runKMA,</span></span>
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1299
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1307
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<pre style="margin: 0;"> <span id="LC1307" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> at the cost it chooses best templates based on kmers</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1456" style="width: 35px; color: rgba(0,0,0,0.3); 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="1464" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -1456,6 +1464,7 @@ int runKMA_MEM(char *templatefilename, char *outputfilename, char *exePrev, int</td>
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1456
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1464
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<pre style="margin: 0;"> <span id="LC1464" class="line" lang="c"> <span class="n" style="color: #333;">bestTemplates</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">matched_templates</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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1457
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1465
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<pre style="margin: 0;"> <span id="LC1465" class="line" lang="c"> </span>
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1458
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<td class="diff-line-num new_line" data-linenumber="1466" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1466
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<pre style="margin: 0;"> <span id="LC1466" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* consider printPair */</span></span>
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1467
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<pre style="margin: 0;">+<span id="LC1467" class="line" lang="c"> <span class="n" style="color: #333;">Nhits</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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1459
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1468
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<pre style="margin: 0;"> <span id="LC1468" class="line" lang="c"> <span class="n" style="color: #333;">t_len</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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1460
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1469
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<pre style="margin: 0;"> <span id="LC1469" class="line" lang="c"> <span class="n" style="color: #333;">read_score</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="1461" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1461
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1470
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<pre style="margin: 0;"> <span id="LC1470" class="line" lang="c"> <span class="k" style="font-weight: 600;">while</span><span class="p">((</span><span class="n" style="color: #333;">rc_flag</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">get_ankers</span><span class="p">(</span><span class="n" style="color: #333;">matched_templates</span><span class="p">,</span> <span class="n" style="color: #333;">qseq_comp</span><span class="p">,</span> <span class="n" style="color: #333;">header</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">flag</span><span class="p">,</span> <span class="n" style="color: #333;">inputfile</span><span class="p">))</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1510" style="width: 35px; color: rgba(0,0,0,0.3); 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="1519" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -1510,8 +1519,21 @@ int runKMA_MEM(char *templatefilename, char *outputfilename, char *exePrev, int</td>
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1510
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<td class="diff-line-num new_line" data-linenumber="1519" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1519
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<pre style="margin: 0;"> <span id="LC1519" class="line" lang="c"> <span class="n" style="color: #333;">updateAllFrag</span><span class="p">(</span><span class="n" style="color: #333;">qseq_r</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="n" style="color: #333;">qseq_r</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">len</span><span class="p">,</span> <span class="n" style="color: #333;">abs</span><span class="p">(</span><span class="n" style="color: #333;">bestHits</span><span class="p">),</span> <span class="n" style="color: #333;">read_score</span><span class="p">,</span> <span class="n" style="color: #333;">best_start_pos</span><span class="p">,</span> <span class="n" style="color: #333;">best_end_pos</span><span class="p">,</span> <span class="n" style="color: #333;">bestTemplates</span><span class="p">,</span> <span class="n" style="color: #333;">header_r</span><span class="p">,</span> <span class="n" style="color: #333;">frag_out_all</span><span class="p">);</span></span>
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1511
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1520
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<pre style="margin: 0;"> <span id="LC1520" class="line" lang="c"> <span class="p">}</span></span>
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1512
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1521
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<pre style="margin: 0;"> <span id="LC1521" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1513" style="width: 35px; color: rgba(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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1522
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<pre style="margin: 0;">+<span id="LC1522" class="line" lang="c"> </span>
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1523
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<pre style="margin: 0;">+<span id="LC1523" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* verbose */</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1524" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1524
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<pre style="margin: 0;">+<span id="LC1524" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">verbose</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">verbose</span><span class="o" style="font-weight: 600;">++</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1024</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1525" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1525
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<pre style="margin: 0;">+<span id="LC1525" class="line" lang="c"> <span class="n" style="color: #333;">Nhits</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">verbose</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1526" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1526
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<pre style="margin: 0;">+<span id="LC1526" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"# Scored %ld query sequences.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">Nhits</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1527" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1527
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<pre style="margin: 0;">+<span id="LC1527" class="line" lang="c"> <span class="n" style="color: #333;">verbose</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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1528
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<pre style="margin: 0;">+<span id="LC1528" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="1513" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1513
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<td class="diff-line-num new_line" data-linenumber="1529" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1529
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<pre style="margin: 0;"> <span id="LC1529" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="1514" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1514
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<td class="diff-line-num new_line" data-linenumber="1530" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1530
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<pre style="margin: 0;"> <span id="LC1530" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1515" style="width: 35px; color: rgba(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="1531" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1531
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<pre style="margin: 0;">+<span id="LC1531" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* verbose */</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1515" style="width: 35px; color: rgba(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="1532" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1532
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<pre style="margin: 0;">+<span id="LC1532" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">verbose</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1515" style="width: 35px; color: rgba(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="1533" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1533
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<pre style="margin: 0;">+<span id="LC1533" class="line" lang="c"> <span class="n" style="color: #333;">Nhits</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">verbose</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1515" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1534" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1534
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<pre style="margin: 0;">+<span id="LC1534" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"# Scored %ld query sequences.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">Nhits</span><span class="p">);</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1515" style="width: 35px; color: rgba(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="1535" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1535
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<pre style="margin: 0;">+<span id="LC1535" class="line" lang="c"> <span class="n" style="color: #333;">verbose</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1515" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1536" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1536
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<pre style="margin: 0;">+<span id="LC1536" class="line" lang="c"> <span class="p">}</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1515" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1515
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<td class="diff-line-num new_line" data-linenumber="1537" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1537
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<pre style="margin: 0;"> <span id="LC1537" class="line" lang="c"> <span class="n" style="color: #333;">kmaPipe</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">inputfile</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">i</span><span class="p">);</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1516" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1516
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<td class="diff-line-num new_line" data-linenumber="1538" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1538
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<pre style="margin: 0;"> <span id="LC1538" class="line" lang="c"> <span class="n" style="color: #333;">status</span> <span class="o" style="font-weight: 600;">|=</span> <span class="n" style="color: #333;">i</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="1517" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1517
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<td class="diff-line-num new_line" data-linenumber="1539" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1539
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<pre style="margin: 0;"> <span id="LC1539" class="line" lang="c"> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2250" style="width: 35px; color: rgba(0,0,0,0.3); 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="2272" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -2250,17 +2272,21 @@ int runKMA_MEM(char *templatefilename, char *outputfilename, char *exePrev, int</td>
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2250
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<td class="diff-line-num new_line" data-linenumber="2272" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2272
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<pre style="margin: 0;"> <span id="LC2272" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">progress</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="2251" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2251
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<td class="diff-line-num new_line" data-linenumber="2273" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2273
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<pre style="margin: 0;"> <span id="LC2273" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"# Progress:</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%3d%%</span><span class="se" style="color: #d14;">\r</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="2252" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2252
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<td class="diff-line-num new_line" data-linenumber="2274" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2274
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<pre style="margin: 0;"> <span id="LC2274" class="line" lang="c"> <span class="n" style="color: #333;">fflush</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">);</span></span>
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<td class="diff-line-num new old_line" data-linenumber="2253" style="width: 35px; color: rgba(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="2275" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2275
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<pre style="margin: 0;">+<span id="LC2275" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">verbose</span><span class="p">)</span> <span class="p">{</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="2253" style="width: 35px; color: rgba(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="2276" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2276
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<pre style="margin: 0;">+<span id="LC2276" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"# Template</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">Score</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">Progress</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2253" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2253
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<td class="diff-line-num new_line" data-linenumber="2277" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2277
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<pre style="margin: 0;"> <span id="LC2277" class="line" lang="c"> <span class="p">}</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2254" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2254
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<td class="diff-line-num new_line" data-linenumber="2278" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2278
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<pre style="margin: 0;"> <span id="LC2278" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">assembly_KMA_Ptr</span> <span class="o" style="font-weight: 600;">==</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">skip_assemble_KMA</span><span class="p">)</span> <span class="p">{</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2255" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2255
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<td class="diff-line-num new_line" data-linenumber="2279" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2279
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<pre style="margin: 0;"> <span id="LC2279" class="line" lang="c"> <span class="n" style="color: #333;">alignLoadPtr</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">alignLoad_skip</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="2256" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2256
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<td class="diff-line-num new_line" data-linenumber="2280" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2280
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<pre style="margin: 0;"> <span id="LC2280" class="line" lang="c"> <span class="p">}</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="2257" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
2257
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<td class="diff-line-num new_line old" data-linenumber="2281" style="width: 35px; color: rgba(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="LC2257" class="line" lang="c"> </span>
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2258
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2281
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<pre style="margin: 0;"> <span id="LC2281" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="n" style="color: #333;">template</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;">template</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">DB_size</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">template</span><span class="p">)</span> <span class="p">{</span></span>
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2259
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2282
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<pre style="margin: 0;"> <span id="LC2282" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">w_scores</span><span class="p">[</span><span class="n" style="color: #333;">template</span><span class="p">]</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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2260
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2283
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<pre style="margin: 0;"> <span id="LC2283" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">progress</span><span class="p">)</span> <span class="p">{</span></span>
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2261
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<td class="diff-line-num new_line" data-linenumber="2284" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2284
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<pre style="margin: 0;"> <span id="LC2284" class="line" lang="c"> <span class="n" style="color: #333;">counter</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">w_scores</span><span class="p">[</span><span class="n" style="color: #333;">template</span><span class="p">];</span></span>
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2262
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2285
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<pre style="margin: 0;"> <span id="LC2285" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"# Progress:</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%3lu%%</span><span class="se" style="color: #d14;">\r</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="mi" style="color: #099;">100</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">counter</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">Nhits</span><span class="p">);</span></span>
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2263
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2286
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<pre style="margin: 0;"> <span id="LC2286" class="line" lang="c"> <span class="n" style="color: #333;">fflush</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">);</span></span>
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2287
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<pre style="margin: 0;">+<span id="LC2287" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">verbose</span><span class="p">)</span> <span class="p">{</span></span>
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2288
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<pre style="margin: 0;">+<span id="LC2288" class="line" lang="c"> <span class="n" style="color: #333;">counter</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">w_scores</span><span class="p">[</span><span class="n" style="color: #333;">template</span><span class="p">];</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2289" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2289
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<pre style="margin: 0;">+<span id="LC2289" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"# %d / %d</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%lu</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%3lu%%</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">template</span><span class="p">,</span> <span class="n" style="color: #333;">DB_size</span><span class="p">,</span> <span class="n" style="color: #333;">w_scores</span><span class="p">[</span><span class="n" style="color: #333;">template</span><span class="p">],</span> <span class="mi" style="color: #099;">100</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">counter</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">Nhits</span><span class="p">);</span></span>
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2290
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<pre style="margin: 0;"> <span id="LC2290" class="line" lang="c"> <span class="p">}</span></span>
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2291
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<pre style="margin: 0;"> <span id="LC2291" class="line" lang="c"> </span>
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2292
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<pre style="margin: 0;"> <span id="LC2292" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* make p_value to see whether assembly is feasable */</span></span>
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<a href="https://salsa.debian.org/med-team/kma/-/commit/2f19ae42ee0599842c05907229fbcefcd490ae07#96f176d59b0bd765be8443801e2c6244ae632120"><strong>runkma.h</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -26,5 +26,5 @@</td>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span> <span class="nf" style="color: #900; font-weight: 600;">ustrdup</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">src</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">n</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">load_DBs_KMA</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;">templatefilename</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">alignment_scores</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">uniq_alignment_scores</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">template_lengths</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">shm</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span> <span class="nf" style="color: #900; font-weight: 600;">nameLoad</span><span class="p">(</span><span class="n" style="color: #333;">Qseqs</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">infile</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">runKMA</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;">templatefilename</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;">outputfilename</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;">exePrev</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ConClave</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">kmersize</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">minlen</span><span class="p">,</span> <span class="n" style="color: #333;">Penalties</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">rewards</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">extendedFeatures</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">ID_t</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">mq</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">scoreT</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">evalue</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">bcd</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ref_fsa</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">print_matrix</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">print_all</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">vcf</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">sam</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nc</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nf</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">shm</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">thread_num</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">runKMA_MEM</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;">templatefilename</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;">outputfilename</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;">exePrev</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ConClave</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">kmersize</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">minlen</span><span class="p">,</span> <span class="n" style="color: #333;">Penalties</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">rewards</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">extendedFeatures</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">ID_t</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">mq</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">scoreT</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">evalue</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">bcd</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ref_fsa</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">print_matrix</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">print_all</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">vcf</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">sam</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nc</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nf</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">shm</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">thread_num</span><span class="p">);</span></span></pre>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">runKMA</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;">templatefilename</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;">outputfilename</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;">exePrev</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ConClave</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">kmersize</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">minlen</span><span class="p">,</span> <span class="n" style="color: #333;">Penalties</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">rewards</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">extendedFeatures</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">ID_t</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">mq</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">scoreT</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">evalue</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">bcd</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ref_fsa</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">print_matrix</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">print_all</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">vcf</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">sam</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nc</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nf</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">shm</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">thread_num</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">int</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">verbose</span></span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">runKMA_MEM</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;">templatefilename</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;">outputfilename</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;">exePrev</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ConClave</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">kmersize</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">minlen</span><span class="p">,</span> <span class="n" style="color: #333;">Penalties</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">rewards</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">extendedFeatures</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">ID_t</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">mq</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">scoreT</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">evalue</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">bcd</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ref_fsa</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">print_matrix</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">print_all</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">vcf</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">sam</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nc</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nf</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">shm</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">thread_num</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">int</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">verbose</span></span><span class="p">);</span></span></pre>
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<a href="https://salsa.debian.org/med-team/kma/-/commit/2f19ae42ee0599842c05907229fbcefcd490ae07#cd8b7c197c9ac04f72eb54b22a8a01d5b1d0391f"><strong>sparse.c</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">@@ -226,7 +226,7 @@ void save_kmers_sparse(const HashMapKMA *templates, HashMap_kmers *foundKmers, C</td>
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<pre style="margin: 0;"> <span id="LC226" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC227" class="line" lang="c"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC228" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC229" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">run_input_sparse</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">HashMapKMA</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">templates</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;">inputfiles</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">fileCount</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">minPhred</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">fiveClip</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">kmersize</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;">trans</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">out</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">run_input_sparse</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">HashMapKMA</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">templates</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;">inputfiles</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">fileCount</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">minPhred</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">fiveClip</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;"><span class="idiff left">threeClip</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">int</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">kmersize</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;">trans</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">out</span><span class="p">)</span> <span class="p">{</span></span>
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230
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230
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<pre style="margin: 0;"> <span id="LC230" class="line" lang="c"> </span>
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231
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231
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<pre style="margin: 0;"> <span id="LC231" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">FASTQ</span><span class="p">,</span> <span class="n" style="color: #333;">fileCounter</span><span class="p">,</span> <span class="n" style="color: #333;">phredCut</span><span class="p">,</span> <span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="n" style="color: #333;">end</span><span class="p">;</span></span>
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232
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232
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<pre style="margin: 0;"> <span id="LC232" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">filename</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="263" style="width: 35px; color: rgba(0,0,0,0.3); 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="263" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -263,7 +263,8 @@ void run_input_sparse(const HashMapKMA *templates, char **inputfiles, int fileCo</td>
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263
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263
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<pre style="margin: 0;"> <span id="LC263" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* trim */</span></span>
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264
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<pre style="margin: 0;"> <span id="LC264" class="line" lang="c"> <span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">qual</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seq</span><span class="p">;</span></span>
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265
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265
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<pre style="margin: 0;"> <span id="LC265" class="line" lang="c"> <span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fiveClip</span><span class="p">;</span></span>
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266
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<pre style="margin: 0;">-<span id="LC266" class="line" lang="c"> <span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">qseq</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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266
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<pre style="margin: 0;">+<span id="LC266" class="line" lang="c"> <span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">qseq</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">threeClip</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC267" class="line" lang="c"> <span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">?</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">end</span><span class="p">;</span></span>
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267
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<pre style="margin: 0;"> <span id="LC268" class="line" lang="c"> <span class="k" style="font-weight: 600;">while</span><span class="p">(</span><span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">seq</span><span class="p">[</span><span class="n" style="color: #333;">end</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">phredCut</span><span class="p">)</span> <span class="p">{</span></span>
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268
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<pre style="margin: 0;"> <span id="LC269" class="line" lang="c"> <span class="o" style="font-weight: 600;">--</span><span class="n" style="color: #333;">end</span><span class="p">;</span></span>
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269
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<pre style="margin: 0;"> <span id="LC270" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="314" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -313,11 +314,11 @@ void run_input_sparse(const HashMapKMA *templates, char **inputfiles, int fileCo</td>
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313
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314
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<pre style="margin: 0;"> <span id="LC314" class="line" lang="c"></span>
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314
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<pre style="margin: 0;"> <span id="LC315" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">save_kmers_sparse_batch</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;">templatefilename</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;">outputfilename</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;">exePrev</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ID_t</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">evalue</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">ss</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">shm</span><span class="p">)</span> <span class="p">{</span></span>
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315
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316
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<pre style="margin: 0;"> <span id="LC316" class="line" lang="c"> </span>
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<pre style="margin: 0;">-<span id="LC316" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">file_len</span><span class="p">,</span> <span class="n" style="color: #333;">stop</span><span class="p">,</span> <span class="n" style="color: #333;">template</span><span class="p">,</span> <span class="n" style="color: #333;">score</span><span class="p">,</span> <span class="n" style="color: #333;">tmp_score</span><span class="p">,</span> <span class="n" style="color: #333;">status</span><span class="p">,</span> <span class="n" style="color: #333;">contamination</span><span class="p">;</span></span>
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317
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<pre style="margin: 0;">-<span id="LC317" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">score_add</span><span class="p">,</span> <span class="n" style="color: #333;">score_tot_add</span><span class="p">,</span> <span class="n" style="color: #333;">deCon</span><span class="p">;</span></span>
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318
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<pre style="margin: 0;">-<span id="LC318" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">Scores</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">Scores_tot</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">w_Scores</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">w_Scores_tot</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">SearchList</span><span class="p">;</span></span>
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317
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<pre style="margin: 0;">+<span id="LC317" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">file_len</span><span class="p">,</span> <span class="n" style="color: #333;">stop</span><span class="p">,</span> <span class="n" style="color: #333;">template</span><span class="p">,</span> <span class="n" style="color: #333;">status</span><span class="p">,</span> <span class="n" style="color: #333;">contamination</span><span class="p">,</span> <span class="n" style="color: #333;">score_add</span><span class="p">,</span> <span class="n" style="color: #333;">deCon</span><span class="p">;</span></span>
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318
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<pre style="margin: 0;">+<span id="LC318" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">Scores</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">w_Scores</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">SearchList</span><span class="p">;</span></span>
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319
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319
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<pre style="margin: 0;"> <span id="LC319" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">template_lengths</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">template_ulengths</span><span class="p">;</span></span>
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320
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<pre style="margin: 0;">-<span id="LC320" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">Ntot</span><span class="p">;</span></span>
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320
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<pre style="margin: 0;">+<span id="LC320" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">Ntot</span><span class="p">,</span> <span class="n" style="color: #333;">score</span><span class="p">,</span> <span class="n" style="color: #333;">tmp_score</span><span class="p">,</span> <span class="n" style="color: #333;">score_tot_add</span><span class="p">;</span></span>
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321
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<pre style="margin: 0;">+<span id="LC321" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">Scores_tot</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">w_Scores_tot</span><span class="p">;</span></span>
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321
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322
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<pre style="margin: 0;"> <span id="LC322" class="line" lang="c"> <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;">template_names</span><span class="p">;</span></span>
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322
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323
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<pre style="margin: 0;"> <span id="LC323" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">expected</span><span class="p">,</span> <span class="n" style="color: #333;">q_value</span><span class="p">,</span> <span class="n" style="color: #333;">p_value</span><span class="p">,</span> <span class="n" style="color: #333;">etta</span><span class="p">,</span> <span class="n" style="color: #333;">depth</span><span class="p">,</span> <span class="n" style="color: #333;">cover</span><span class="p">,</span> <span class="n" style="color: #333;">query_cover</span><span class="p">;</span></span>
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323
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324
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<pre style="margin: 0;"> <span id="LC324" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">tot_depth</span><span class="p">,</span> <span class="n" style="color: #333;">tot_cover</span><span class="p">,</span> <span class="n" style="color: #333;">tot_query_cover</span><span class="p">,</span> <span class="n" style="color: #333;">tmp_depth</span><span class="p">,</span> <span class="n" style="color: #333;">tmp_cover</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="359" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -359,7 +360,7 @@ int save_kmers_sparse_batch(char *templatefilename, char *outputfilename, char *</td>
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359
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360
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<pre style="margin: 0;"> <span id="LC360" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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360
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361
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<pre style="margin: 0;"> <span id="LC361" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">hashMapKMA_load</span><span class="p">(</span><span class="n" style="color: #333;">templates</span><span class="p">,</span> <span class="n" style="color: #333;">templatefile</span><span class="p">,</span> <span class="n" style="color: #333;">templatefilename</span><span class="p">))</span> <span class="p">{</span></span>
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361
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362
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<pre style="margin: 0;"> <span id="LC362" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"Wrong format of DB.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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362
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<pre style="margin: 0;">-<span id="LC362" class="line" lang="c"> <span class="n" style="color: #333;">exit</span><span class="p">(</span><span class="mi" style="color: #099;"><span class="idiff left right">2</span></span><span class="p">);</span></span>
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363
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<pre style="margin: 0;">+<span id="LC363" class="line" lang="c"> <span class="n" style="color: #333;">exit</span><span class="p">(</span><span class="mi" style="color: #099;"><span class="idiff left right">1</span></span><span class="p">);</span></span>
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363
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<pre style="margin: 0;"> <span id="LC364" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC365" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC366" class="line" lang="c"> <span class="n" style="color: #333;">fclose</span><span class="p">(</span><span class="n" style="color: #333;">templatefile</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">@@ -416,9 +417,9 @@ int save_kmers_sparse_batch(char *templatefilename, char *outputfilename, char *</td>
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<pre style="margin: 0;"> <span id="LC417" class="line" lang="c"> <span class="n" style="color: #333;">t0</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">clock</span><span class="p">();</span></span>
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<pre style="margin: 0;"> <span id="LC418" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"# Finding best matches and output results.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC419" class="line" lang="c"> </span>
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<pre style="margin: 0;">-<span id="LC419" class="line" lang="c"> <span class="n" style="color: #333;">Scores</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">calloc</span><span class="p">(</span><span class="n" style="color: #333;">templates</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">DB_size</span><span class="p">,</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right">int</span></span><span class="p">));</span></span>
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<pre style="margin: 0;">-<span id="LC420" class="line" lang="c"> <span class="n" style="color: #333;">Scores_tot</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">calloc</span><span class="p">(</span><span class="n" style="color: #333;">templates</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">DB_size</span><span class="p">,</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right">int</span></span><span class="p">));</span></span>
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<pre style="margin: 0;">-<span id="LC421" class="line" lang="c"> <span class="n" style="color: #333;">SearchList</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">malloc</span><span class="p">(</span><span class="n" style="color: #333;">templates</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">DB_size</span> <span class="o" style="font-weight: 600;">*</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right">int</span></span><span class="p">));</span></span>
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<pre style="margin: 0;">+<span id="LC420" class="line" lang="c"> <span class="n" style="color: #333;">Scores</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">calloc</span><span class="p">(</span><span class="n" style="color: #333;">templates</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">DB_size</span><span class="p">,</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right">unsigned</span></span><span class="p">));</span></span>
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<pre style="margin: 0;">+<span id="LC421" class="line" lang="c"> <span class="n" style="color: #333;">Scores_tot</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">calloc</span><span class="p">(</span><span class="n" style="color: #333;">templates</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">DB_size</span><span class="p">,</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">long</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff right">unsigned</span></span><span class="p">));</span></span>
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<pre style="margin: 0;">+<span id="LC422" class="line" lang="c"> <span class="n" style="color: #333;">SearchList</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">malloc</span><span class="p">(</span><span class="n" style="color: #333;">templates</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">DB_size</span> <span class="o" style="font-weight: 600;">*</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right">unsigned</span></span><span class="p">));</span></span>
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<pre style="margin: 0;"> <span id="LC423" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">Scores</span> <span class="o" style="font-weight: 600;">||</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">Scores_tot</span> <span class="o" style="font-weight: 600;">||</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">SearchList</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC424" class="line" lang="c"> <span class="n" style="color: #333;">ERROR</span><span class="p">();</span></span>
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<pre style="margin: 0;"> <span id="LC425" class="line" lang="c"> <span class="p">}</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -439,8 +440,8 @@ int save_kmers_sparse_batch(char *templatefilename, char *outputfilename, char *</td>
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<pre style="margin: 0;"> <span id="LC440" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC441" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"# Total number of matches: %lu of %lu kmers</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">Nhits</span><span class="p">.</span><span class="n" style="color: #333;">tot</span><span class="p">,</span> <span class="n" style="color: #333;">Ntot</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC442" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* copy scores */</span></span>
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<pre style="margin: 0;">-<span id="LC442" class="line" lang="c"> <span class="n" style="color: #333;">w_Scores</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">smalloc</span><span class="p">(</span><span class="n" style="color: #333;">templates</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">DB_size</span> <span class="o" style="font-weight: 600;">*</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right">int</span></span><span class="p">));</span></span>
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<pre style="margin: 0;">-<span id="LC443" class="line" lang="c"> <span class="n" style="color: #333;">w_Scores_tot</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">smalloc</span><span class="p">(</span><span class="n" style="color: #333;">templates</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">DB_size</span> <span class="o" style="font-weight: 600;">*</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right">int</span></span><span class="p">));</span></span>
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<pre style="margin: 0;">+<span id="LC443" class="line" lang="c"> <span class="n" style="color: #333;">w_Scores</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">smalloc</span><span class="p">(</span><span class="n" style="color: #333;">templates</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">DB_size</span> <span class="o" style="font-weight: 600;">*</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right">unsigned</span></span><span class="p">));</span></span>
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<pre style="margin: 0;">+<span id="LC444" class="line" lang="c"> <span class="n" style="color: #333;">w_Scores_tot</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">smalloc</span><span class="p">(</span><span class="n" style="color: #333;">templates</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">DB_size</span> <span class="o" style="font-weight: 600;">*</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">long</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff right">unsigned</span></span><span class="p">));</span></span>
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<pre style="margin: 0;"> <span id="LC445" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC446" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">templates</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">DB_size</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC447" class="line" lang="c"> <span class="n" style="color: #333;">w_Scores</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Scores</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="597" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -596,7 +597,7 @@ int save_kmers_sparse_batch(char *templatefilename, char *outputfilename, char *</td>
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596
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<pre style="margin: 0;"> <span id="LC597" class="line" lang="c"> <span class="n" style="color: #333;">tot_query_cover</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">100</span><span class="p">.</span><span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="n" style="color: #333;">Scores_tot</span><span class="p">[</span><span class="n" style="color: #333;">template</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">score_tot_add</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">Ntot</span><span class="p">;</span></span>
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598
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<pre style="margin: 0;"> <span id="LC598" class="line" lang="c"> </span>
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598
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599
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<pre style="margin: 0;"> <span id="LC599" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* output results */</span></span>
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<pre style="margin: 0;">-<span id="LC599" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">sparse_out</span><span class="p">,</span> <span class="s" style="color: #d14;">"%s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%d</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%<span class="idiff left right">d</span></span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%d</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%d</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%8.2f</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%8.2f</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%8.2f</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%8.2f</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%8.2f</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%8.2f</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%f</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%e</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> </span>
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<pre style="margin: 0;">+<span id="LC600" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">sparse_out</span><span class="p">,</span> <span class="s" style="color: #d14;">"%s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%d</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%<span class="idiff left right">lu</span></span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%d</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%d</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%8.2f</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%8.2f</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%8.2f</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%8.2f</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%8.2f</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%8.2f</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%f</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%e</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> </span>
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601
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<pre style="margin: 0;"> <span id="LC601" class="line" lang="c"> <span class="n" style="color: #333;">template_names</span><span class="p">[</span><span class="n" style="color: #333;">template</span><span class="p">],</span> <span class="n" style="color: #333;">template</span><span class="p">,</span> <span class="n" style="color: #333;">score</span><span class="p">,</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)</span> <span class="n" style="color: #333;">expected</span><span class="p">,</span> <span class="n" style="color: #333;">template_lengths</span><span class="p">[</span><span class="n" style="color: #333;">template</span><span class="p">],</span> <span class="n" style="color: #333;">query_cover</span><span class="p">,</span> <span class="n" style="color: #333;">cover</span><span class="p">,</span> <span class="n" style="color: #333;">depth</span><span class="p">,</span> <span class="n" style="color: #333;">tot_query_cover</span><span class="p">,</span> <span class="n" style="color: #333;">tot_cover</span><span class="p">,</span> <span class="n" style="color: #333;">tot_depth</span><span class="p">,</span> <span class="n" style="color: #333;">q_value</span><span class="p">,</span> <span class="n" style="color: #333;">p_value</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC602" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC603" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* update scores */</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="743" style="width: 35px; color: rgba(0,0,0,0.3); 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="744" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -743,7 +744,7 @@ int save_kmers_sparse_batch(char *templatefilename, char *outputfilename, char *</td>
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743
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<pre style="margin: 0;"> <span id="LC744" class="line" lang="c"> <span class="n" style="color: #333;">tot_cover</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">100</span><span class="p">.</span><span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">Scores</span><span class="p">[</span><span class="n" style="color: #333;">template</span><span class="p">]</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">template_ulengths</span><span class="p">[</span><span class="n" style="color: #333;">template</span><span class="p">];</span></span>
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<pre style="margin: 0;"> <span id="LC745" class="line" lang="c"> <span class="n" style="color: #333;">tot_depth</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">.</span><span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">Scores_tot</span><span class="p">[</span><span class="n" style="color: #333;">template</span><span class="p">]</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">template_lengths</span><span class="p">[</span><span class="n" style="color: #333;">template</span><span class="p">];</span></span>
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<pre style="margin: 0;"> <span id="LC746" class="line" lang="c"> <span class="n" style="color: #333;">tot_query_cover</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">100</span><span class="p">.</span><span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">Scores_tot</span><span class="p">[</span><span class="n" style="color: #333;">template</span><span class="p">]</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">Ntot</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC746" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">sparse_out</span><span class="p">,</span> <span class="s" style="color: #d14;">"%s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%d</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%<span class="idiff left right">d</span></span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%d</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%d</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%8.2f</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%8.2f</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%8.2f</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%8.2f</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%8.2f</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%8.2f</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%8.2f</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%4.1e</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> </span>
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<pre style="margin: 0;">+<span id="LC747" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">sparse_out</span><span class="p">,</span> <span class="s" style="color: #d14;">"%s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%d</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%<span class="idiff left right">lu</span></span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%d</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%d</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%8.2f</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%8.2f</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%8.2f</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%8.2f</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%8.2f</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%8.2f</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%8.2f</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%4.1e</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> </span>
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<pre style="margin: 0;"> <span id="LC748" class="line" lang="c"> <span class="n" style="color: #333;">template_names</span><span class="p">[</span><span class="n" style="color: #333;">template</span><span class="p">],</span> <span class="n" style="color: #333;">template</span><span class="p">,</span> <span class="n" style="color: #333;">score</span><span class="p">,</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)</span> <span class="n" style="color: #333;">expected</span><span class="p">,</span> <span class="n" style="color: #333;">template_lengths</span><span class="p">[</span><span class="n" style="color: #333;">template</span><span class="p">],</span> <span class="n" style="color: #333;">query_cover</span><span class="p">,</span> <span class="n" style="color: #333;">cover</span><span class="p">,</span> <span class="n" style="color: #333;">depth</span><span class="p">,</span> <span class="n" style="color: #333;">tot_query_cover</span><span class="p">,</span> <span class="n" style="color: #333;">tot_cover</span><span class="p">,</span> <span class="n" style="color: #333;">tot_depth</span><span class="p">,</span> <span class="n" style="color: #333;">q_value</span><span class="p">,</span> <span class="n" style="color: #333;">p_value</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC749" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC750" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* update scores */</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">@@ -24,5 +24,5 @@</td>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">translateToKmersAndDump</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">Kmers</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">n</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">max</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">seqlen</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">kmersize</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">mask</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">prefix</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">prefix_len</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">out</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">**</span> <span class="nf" style="color: #900; font-weight: 600;">load_DBs_Sparse</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;">templatefilename</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">template_lengths</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">template_ulengths</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">shm</span><span class="p">);</span></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;">void</span> <span class="nf" style="color: #900; font-weight: 600;">save_kmers_sparse</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">HashMapKMA</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">templates</span><span class="p">,</span> <span class="n" style="color: #333;">HashMap_kmers</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">foundKmers</span><span class="p">,</span> <span class="n" style="color: #333;">CompKmers</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">compressor</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">run_input_sparse</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">HashMapKMA</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">templates</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;">inputfiles</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">fileCount</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">minPhred</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">fiveClip</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">kmersize</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;">trans</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">out</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">run_input_sparse</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">HashMapKMA</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">templates</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;">inputfiles</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">fileCount</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">minPhred</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">fiveClip</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;"><span class="idiff left">threeClip</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">int</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">kmersize</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;">trans</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">out</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">save_kmers_sparse_batch</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;">templatefilename</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;">outputfilename</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;">exePrev</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ID_t</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">evalue</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">ss</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">shm</span><span class="p">);</span></span></pre>
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<a href="https://salsa.debian.org/med-team/kma/-/commit/2f19ae42ee0599842c05907229fbcefcd490ae07#f80652dda49a7117428c0f92935664fc8cd4e2d1"><strong>spltdb.c</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">@@ -394,7 +394,7 @@ unsigned get_ankers_spltDB(int *infoSize, int *out_Tem, CompDNA *qseq, Qseqs *he</td>
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<pre style="margin: 0;"> <span id="LC394" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">num</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC395" class="line" lang="c"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC396" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC397" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">runKMA_spltDB</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;">templatefilenames</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">targetNum</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;">outputfilename</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">argc</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">argv</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ConClave</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">kmersize</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">minlen</span><span class="p">,</span> <span class="n" style="color: #333;">Penalties</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">rewards</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">extendedFeatures</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">ID_t</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">mq</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">scoreT</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">evalue</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">bcd</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ref_fsa</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">print_matrix</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">print_all</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">vcf</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">sam</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nc</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nf</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">shm</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">thread_num</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC397" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">runKMA_spltDB</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;">templatefilenames</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">targetNum</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;">outputfilename</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">argc</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">argv</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ConClave</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">kmersize</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">minlen</span><span class="p">,</span> <span class="n" style="color: #333;">Penalties</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">rewards</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">extendedFeatures</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">ID_t</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">mq</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">scoreT</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">evalue</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">bcd</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ref_fsa</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">print_matrix</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">print_all</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">vcf</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">sam</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nc</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nf</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">shm</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">thread_num</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">int</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">verbose</span></span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC398" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC399" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* https://www.youtube.com/watch?v=LtXEMwSG5-8 */</span></span>
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<pre style="margin: 0;"> <span id="LC400" class="line" lang="c"> </span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -605,6 +605,7 @@ int runKMA_spltDB(char **templatefilenames, int targetNum, char *outputfilename,</td>
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<pre style="margin: 0;"> <span id="LC605" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC606" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC607" class="line" lang="c"> </span>
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<pre style="margin: 0;">+<span id="LC608" class="line" lang="c"> <span class="n" style="color: #333;">Nhits</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="LC609" class="line" lang="c"> <span class="n" style="color: #333;">target</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="LC610" class="line" lang="c"> <span class="n" style="color: #333;">targetScore</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="LC611" class="line" lang="c"> <span class="n" style="color: #333;">rc_flag</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -675,6 +676,13 @@ int runKMA_spltDB(char **templatefilenames, int targetNum, char *outputfilename,</td>
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<pre style="margin: 0;"> <span id="LC676" class="line" lang="c"> <span class="n" style="color: #333;">updateAllFrag</span><span class="p">(</span><span class="n" style="color: #333;">qseq_r</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="n" style="color: #333;">qseq_r</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">len</span><span class="p">,</span> <span class="n" style="color: #333;">abs</span><span class="p">(</span><span class="n" style="color: #333;">bestHits</span><span class="p">),</span> <span class="n" style="color: #333;">read_score</span><span class="p">,</span> <span class="n" style="color: #333;">best_start_pos</span><span class="p">,</span> <span class="n" style="color: #333;">best_end_pos</span><span class="p">,</span> <span class="n" style="color: #333;">bestTemplates</span><span class="p">,</span> <span class="n" style="color: #333;">header_r</span><span class="p">,</span> <span class="n" style="color: #333;">frag_out_all</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC677" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC678" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC679" class="line" lang="c"> </span>
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<pre style="margin: 0;">+<span id="LC680" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* verbose */</span></span>
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<pre style="margin: 0;">+<span id="LC681" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">verbose</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">verbose</span><span class="o" style="font-weight: 600;">++</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1024</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC682" class="line" lang="c"> <span class="n" style="color: #333;">Nhits</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">verbose</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC683" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"# Scored %ld query sequences.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">Nhits</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC684" class="line" lang="c"> <span class="n" style="color: #333;">verbose</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC685" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC686" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC687" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC688" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* remove inferior read matches */</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">@@ -760,6 +768,12 @@ int runKMA_spltDB(char **templatefilenames, int targetNum, char *outputfilename,</td>
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<pre style="margin: 0;"> <span id="LC768" class="line" lang="c"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">uPtr</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC769" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC770" class="line" lang="c"> <span class="p">}</span></span>
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771
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<pre style="margin: 0;">+<span id="LC771" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* verbose */</span></span>
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772
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<pre style="margin: 0;">+<span id="LC772" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">verbose</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="773" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
773
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<pre style="margin: 0;">+<span id="LC773" class="line" lang="c"> <span class="n" style="color: #333;">Nhits</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">verbose</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="774" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
774
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<pre style="margin: 0;">+<span id="LC774" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"# Scored %ld query sequences.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">Nhits</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="775" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
775
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<pre style="margin: 0;">+<span id="LC775" class="line" lang="c"> <span class="n" style="color: #333;">verbose</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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776
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<pre style="margin: 0;">+<span id="LC776" class="line" lang="c"> <span class="p">}</span></span>
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763
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777
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<pre style="margin: 0;"> <span id="LC777" class="line" lang="c"> </span>
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764
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778
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<pre style="margin: 0;"> <span id="LC778" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* get fragmentCount */</span></span>
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765
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779
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<pre style="margin: 0;"> <span id="LC779" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">extendedFeatures</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1490" style="width: 35px; color: rgba(0,0,0,0.3); 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="1504" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1490,6 +1504,8 @@ int runKMA_spltDB(char **templatefilenames, int targetNum, char *outputfilename,</td>
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1490
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1504
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<pre style="margin: 0;"> <span id="LC1504" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">progress</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="1491" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1491
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<td class="diff-line-num new_line" data-linenumber="1505" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1505
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<pre style="margin: 0;"> <span id="LC1505" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"# Progress:</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%3d%%</span><span class="se" style="color: #d14;">\r</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="1492" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1492
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<td class="diff-line-num new_line" data-linenumber="1506" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1506
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<pre style="margin: 0;"> <span id="LC1506" class="line" lang="c"> <span class="n" style="color: #333;">fflush</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">);</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1493" style="width: 35px; color: rgba(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="1507" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1507
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<pre style="margin: 0;">+<span id="LC1507" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">verbose</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1508" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1508
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<pre style="margin: 0;">+<span id="LC1508" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"# Template</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">Score</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">Progress</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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1493
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1509
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<pre style="margin: 0;"> <span id="LC1509" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="1494" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1494
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1510
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<pre style="margin: 0;"> <span id="LC1510" class="line" lang="c"> </span>
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<td class="diff-line-num old_line" data-linenumber="1495" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1495
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<td class="diff-line-num new_line" data-linenumber="1511" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1511
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<pre style="margin: 0;"> <span id="LC1511" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* get index, seq and names on the fly */</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1583" style="width: 35px; color: rgba(0,0,0,0.3); 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="1599" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -1583,6 +1599,9 @@ int runKMA_spltDB(char **templatefilenames, int targetNum, char *outputfilename,</td>
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<td class="diff-line-num old_line" data-linenumber="1583" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1583
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<td class="diff-line-num new_line" data-linenumber="1599" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1599
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<pre style="margin: 0;"> <span id="LC1599" class="line" lang="c"> <span class="n" style="color: #333;">counter</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">w_scores</span><span class="p">[</span><span class="n" style="color: #333;">template</span><span class="p">];</span></span>
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<td class="diff-line-num old_line" data-linenumber="1584" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1584
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<td class="diff-line-num new_line" data-linenumber="1600" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1600
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<pre style="margin: 0;"> <span id="LC1600" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"# Progress:</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%3lu%%</span><span class="se" style="color: #d14;">\r</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="mi" style="color: #099;">100</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">counter</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">Nhits</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="1585" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1585
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<td class="diff-line-num new_line" data-linenumber="1601" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1601
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<pre style="margin: 0;"> <span id="LC1601" class="line" lang="c"> <span class="n" style="color: #333;">fflush</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC1602" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">verbose</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC1603" class="line" lang="c"> <span class="n" style="color: #333;">counter</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">w_scores</span><span class="p">[</span><span class="n" style="color: #333;">template</span><span class="p">];</span></span>
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1604
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<pre style="margin: 0;">+<span id="LC1604" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"# %d / %d</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%lu</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%3lu%%</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">template</span><span class="p">,</span> <span class="n" style="color: #333;">DB_size</span><span class="p">,</span> <span class="n" style="color: #333;">w_scores</span><span class="p">[</span><span class="n" style="color: #333;">template</span><span class="p">],</span> <span class="mi" style="color: #099;">100</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">counter</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">Nhits</span><span class="p">);</span></span>
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1605
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<pre style="margin: 0;"> <span id="LC1605" class="line" lang="c"> <span class="p">}</span></span>
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1606
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<pre style="margin: 0;"> <span id="LC1606" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC1607" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* make p_value to see whether assembly is feasable */</span></span>
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<a href="https://salsa.debian.org/med-team/kma/-/commit/2f19ae42ee0599842c05907229fbcefcd490ae07#e55b6b603fd8c696cd5ece7be98d78898a9ee58f"><strong>spltdb.h</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -35,4 +35,4 @@ struct spltDBbuff {</td>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">print_ankers_spltDB</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">out_Tem</span><span class="p">,</span> <span class="n" style="color: #333;">CompDNA</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">rc_flag</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Qseqs</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">header</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">flag</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">out</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">print_ankers_Sparse_spltDB</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">out_Tem</span><span class="p">,</span> <span class="n" style="color: #333;">CompDNA</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">rc_flag</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Qseqs</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">header</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">flag</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">out</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="nf" style="color: #900; font-weight: 600;">get_ankers_spltDB</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">infoSize</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">out_Tem</span><span class="p">,</span> <span class="n" style="color: #333;">CompDNA</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq</span><span class="p">,</span> <span class="n" style="color: #333;">Qseqs</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">header</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">flag</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">inputfile</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">runKMA_spltDB</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;">templatefilenames</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">targetNum</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;">outputfilename</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">argc</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">argv</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ConClave</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">kmersize</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">minlen</span><span class="p">,</span> <span class="n" style="color: #333;">Penalties</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">rewards</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">extendedFeatures</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">ID_t</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">mq</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">scoreT</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">evalue</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">bcd</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ref_fsa</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">print_matrix</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">print_all</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">vcf</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">sam</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nc</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nf</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">shm</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">thread_num</span><span class="p">);</span></span></pre>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">runKMA_spltDB</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;">templatefilenames</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">targetNum</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;">outputfilename</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">argc</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">argv</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ConClave</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">kmersize</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">minlen</span><span class="p">,</span> <span class="n" style="color: #333;">Penalties</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">rewards</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">extendedFeatures</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">ID_t</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">mq</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">scoreT</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">evalue</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">bcd</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ref_fsa</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">print_matrix</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">print_all</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">vcf</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">sam</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nc</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nf</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">shm</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">thread_num</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">int</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">verbose</span></span><span class="p">);</span></span></pre>
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<a href="https://salsa.debian.org/med-team/kma/-/commit/2f19ae42ee0599842c05907229fbcefcd490ae07#2d1dba06c7f4b4c2f13e05d40a391d5330c68ce4"><strong>version.h</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -17,4 +17,4 @@</td>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * limitations under the License.</span></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">*/</span></span>
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<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="cp" style="color: #999; font-weight: 600;">#define KMA_VERSION "1.2.2<span class="idiff left right">2</span>"</span></span></pre>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define KMA_VERSION "1.2.2<span class="idiff left right">5</span>"</span></span></pre>
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