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<h3>
Nilesh Patra 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>
<li>
<strong><a href="https://salsa.debian.org/med-team/kma/-/commit/5f0f33279035adaa9d300bd1041d8fbff645219b">5f0f3327</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-10-04T17:00:57+05:30</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 1.3.4</pre>
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<h4>10 changed files:</h4>
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<li class="file-stats">
<a href="#836efb6e25a091dcb4ff8e1dbb2f0be6a5cbf14c">
Makefile
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<li class="file-stats">
<a href="#e9055e7402f2a5fcdae1e9dbca80154ea7a9b426">
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+
db.c
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<li class="file-stats">
<a href="#c6094033a6a88ccec0d79878461e205d3414e446">
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+
db.h
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<li class="file-stats">
<a href="#5bb411548ec4b39482e6de83d3ad98f29b1162b1">
kma.c
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<li class="file-stats">
<a href="#406e031b8824ea26ae0bf4d7579a1d89e3fb5906">
main.c
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<li class="file-stats">
<a href="#088a2f1aaa170cd721dbae6f4b2bcb8239c7119a">
mt1.c
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<li class="file-stats">
<a href="#76d4a085858e48da0f768edd95269019d42998c9">
printconsensus.c
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<li class="file-stats">
<a href="#ca9efd475143efe0a1b0464c67f49900d98ca75a">
runkma.c
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<li class="file-stats">
<a href="#f80652dda49a7117428c0f92935664fc8cd4e2d1">
spltdb.c
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<li class="file-stats">
<a href="#2d1dba06c7f4b4c2f13e05d40a391d5330c68ce4">
version.h
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<h4>Changes:</h4>
<li id="836efb6e25a091dcb4ff8e1dbb2f0be6a5cbf14c">
<a href="https://salsa.debian.org/med-team/kma/-/commit/5f0f33279035adaa9d300bd1041d8fbff645219b#836efb6e25a091dcb4ff8e1dbb2f0be6a5cbf14c"><strong>Makefile</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="make"><span class="nv" style="color: #008080;">CFLAGS</span> <span class="o" style="font-weight: 600;">?=</span> <span class="nt" style="color: #000080;">-Wall</span> <span class="nt" style="color: #000080;">-O3</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="make"><span class="nv" style="color: #008080;">CFLAGS</span> <span class="o" style="font-weight: 600;">+=</span> <span class="nt" style="color: #000080;">-std</span><span class="o" style="font-weight: 600;">=</span>c99</span>
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<td class="diff-line-num new_line old" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="make"><span class="nv" style="color: #008080;">LIBS</span> <span class="o" style="font-weight: 600;">=</span> align.o alnfrags.o ankers.o assembly.o chain.o compdna.o compkmers.o compress.o decon.o dist.o ef.o filebuff.o frags.o hashmap.o hashmapcci.o hashmapkma.o hashmapkmers.o hashtable.o index.o kma.o kmapipe.o kmeranker.o kmers.o kmmap.o loadupdate.o makeindex.o matrix.o mt1.o nw.o pherror.o printconsensus.o qseqs.o qualcheck.o runinput.o runkma.o sam.o savekmers.o seq2fasta.o seqmenttree.o seqparse.o shm.o sparse.o spltdb.o stdnuc.o stdstat.o tmp.o update.o updateindex.o updatescores.o valueshash.o vcf.o xml.o</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="make"><span class="nv" style="color: #008080;">LIBS</span> <span class="o" style="font-weight: 600;">=</span> align.o alnfrags.o ankers.o assembly.o chain.o compdna.o compkmers.o compress.o d<span class="idiff left right">b.o d</span>econ.o dist.o ef.o filebuff.o frags.o hashmap.o hashmapcci.o hashmapkma.o hashmapkmers.o hashtable.o index.o kma.o kmapipe.o kmeranker.o kmers.o kmmap.o loadupdate.o makeindex.o matrix.o mt1.o nw.o pherror.o printconsensus.o qseqs.o qualcheck.o runinput.o runkma.o sam.o savekmers.o seq2fasta.o seqmenttree.o seqparse.o shm.o sparse.o spltdb.o stdnuc.o stdstat.o tmp.o update.o updateindex.o updatescores.o valueshash.o vcf.o xml.o</span>
</pre>
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<td class="diff-line-num new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="make"><span class="nv" style="color: #008080;">PROGS</span> <span class="o" style="font-weight: 600;">=</span> kma kma_index kma_shm kma_update</span>
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<td class="diff-line-num new_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="make"></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="make"><span class="nl">.c .o</span><span class="o" style="font-weight: 600;">:</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="34" style="width: 35px; color: rgba(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="34" style="width: 35px; color: rgba(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">@@ -34,6 +34,7 @@ chain.o: chain.h penalties.h pherror.h stdstat.h</td>
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<td class="diff-line-num new_line" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="make"><span class="nl">compdna.o</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">compdna.h pherror.h stdnuc.h</span></span>
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<td class="diff-line-num old_line" data-linenumber="35" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="35" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="make"><span class="nl">compkmers.o</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">compkmers.h pherror.h</span></span>
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<td class="diff-line-num new_line" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="make"><span class="nl">compress.o</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">compress.h hashmap.h hashmapkma.h pherror.h valueshash.h</span></span>
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<td class="diff-line-num new new_line" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="make"><span class="nl">db.o</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">db.h hashmapkma.h pherror.h stdstat.h</span></span>
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<td class="diff-line-num new_line" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="make"><span class="nl">decon.o</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">decon.h compdna.h filebuff.h hashmapkma.h seqparse.h stdnuc.h qseqs.h updateindex.h</span></span>
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<td class="diff-line-num new_line" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="make"><span class="nl">dist.o</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">dist.h hashmapkma.h matrix.h pherror.h</span></span>
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<td class="diff-line-num new_line" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="make"><span class="nl">ef.o</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">ef.h assembly.h stdnuc.h vcf.h version.h</span></span>
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<li id="e9055e7402f2a5fcdae1e9dbca80154ea7a9b426">
<a href="https://salsa.debian.org/med-team/kma/-/commit/5f0f33279035adaa9d300bd1041d8fbff645219b#e9055e7402f2a5fcdae1e9dbca80154ea7a9b426"><strong>db.c</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/* Philip T.L.C. Clausen Jan 2017 plan@dtu.dk */</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/*</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * Copyright (c) 2017, Philip Clausen, Technical University of Denmark</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * All rights reserved.</span></span>
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<pre style="margin: 0;">+<span id="LC6" 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="LC7" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * Licensed under the Apache License, Version 2.0 (the "License");</span></span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * you may not use this file except in compliance with the License.</span></span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * You may obtain a copy of the License at</span></span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * http://www.apache.org/licenses/LICENSE-2.0</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * Unless required by applicable law or agreed to in writing, software</span></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * distributed under the License is distributed on an "AS IS" BASIS,</span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.</span></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * See the License for the specific language governing permissions and</span></span>
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17
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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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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">*/</span></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define _XOPEN_SOURCE 600</span></span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <limits.h></span></span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <stdio.h></span></span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <stdlib.h></span></span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <string.h></span></span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "db.h"</span></span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "hashmapkma.h"</span></span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "pherror.h"</span></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "stdstat.h"</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;">dbInfo</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;">filename</span><span class="p">)</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="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">bases</span><span class="p">[</span><span class="mi" style="color: #099;">6</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"ACGTN-"</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC32" 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;">filename_len</span><span class="p">,</span> <span class="n" style="color: #333;">min</span><span class="p">,</span> <span class="n" style="color: #333;">max</span><span class="p">,</span> <span class="n" style="color: #333;">index</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC33" 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;">values</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">value_index</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;">short</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;">values_s</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC35" 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;">ntcount</span><span class="p">,</span> <span class="n" style="color: #333;">prefix</span><span class="p">,</span> <span class="n" style="color: #333;">ntax</span><span class="p">,</span> <span class="n" style="color: #333;">v_index</span><span class="p">,</span> <span class="n" style="color: #333;">n</span><span class="p">,</span> <span class="n" style="color: #333;">size</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC36" 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;">value_index_l</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;">double</span> <span class="n" style="color: #333;">mean</span><span class="p">,</span> <span class="n" style="color: #333;">var</span><span class="p">,</span> <span class="n" style="color: #333;">tmp</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;">char</span> <span class="n" style="color: #333;">Prefix</span><span class="p">[</span><span class="mi" style="color: #099;">33</span><span class="p">];</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">dbfile</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="c"> <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>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="c"> </span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* print DB name */</span></span>
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<pre style="margin: 0;">+<span id="LC43" 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;">"DB:</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%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;">filename</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="c"> </span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* get # nucleotides */</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="c"> <span class="n" style="color: #333;">filename_len</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">strlen</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="c"> <span class="n" style="color: #333;">strcpy</span><span class="p">(</span><span class="n" style="color: #333;">filename</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">filename_len</span><span class="p">,</span> <span class="s" style="color: #d14;">".seq.b"</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="c"> <span class="n" style="color: #333;">dbfile</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sfopen</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="p">,</span> <span class="s" style="color: #d14;">"rb"</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="c"> <span class="n" style="color: #333;">fseek</span><span class="p">(</span><span class="n" style="color: #333;">dbfile</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">SEEK_END</span><span class="p">);</span></span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="c"> <span class="n" style="color: #333;">ntcount</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">4</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">ftell</span><span class="p">(</span><span class="n" style="color: #333;">dbfile</span><span class="p">);</span></span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="c"> <span class="n" style="color: #333;">fclose</span><span class="p">(</span><span class="n" style="color: #333;">dbfile</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="52" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="c"> <span class="n" style="color: #333;">filename</span><span class="p">[</span><span class="n" style="color: #333;">filename_len</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="53" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
53
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<pre style="margin: 0;">+<span id="LC53" 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;">"# nucleotides:</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%lu</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;">ntcount</span><span class="p">);</span></span>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="c"> </span>
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<td class="diff-line-num new new_line" data-linenumber="55" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* load database */</span></span>
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<td class="diff-line-num new new_line" data-linenumber="56" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="c"> <span class="n" style="color: #333;">strcpy</span><span class="p">(</span><span class="n" style="color: #333;">filename</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">filename_len</span><span class="p">,</span> <span class="s" style="color: #d14;">".comp.b"</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="57" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="c"> <span class="n" style="color: #333;">dbfile</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sfopen</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="p">,</span> <span class="s" style="color: #d14;">"rb"</span> <span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="58" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="c"> <span class="n" style="color: #333;">templates</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">smalloc</span><span class="p">(</span><span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">HashMapKMA</span><span class="p">));</span></span>
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<td class="diff-line-num new new_line" data-linenumber="59" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
59
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<pre style="margin: 0;">+<span id="LC59" 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;">dbfile</span><span class="p">,</span> <span class="n" style="color: #333;">filename</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="p">{</span></span>
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60
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<pre style="margin: 0;">+<span id="LC60" 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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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="c"> <span class="n" style="color: #333;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="c"> <span class="p">}</span></span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="c"> <span class="n" style="color: #333;">fclose</span><span class="p">(</span><span class="n" style="color: #333;">dbfile</span><span class="p">);</span></span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="c"> <span class="n" style="color: #333;">filename</span><span class="p">[</span><span class="n" style="color: #333;">filename_len</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="c"> </span>
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<td class="diff-line-num new new_line" data-linenumber="66" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* get basic statistics */</span></span>
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<td class="diff-line-num new new_line" data-linenumber="67" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
67
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<pre style="margin: 0;">+<span id="LC67" 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;">"# templates:</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%d</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;">templates</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">DB_size</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="68" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
68
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<pre style="margin: 0;">+<span id="LC68" 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;">"k:</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%d</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;">templates</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">kmersize</span><span class="p">);</span></span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* get prefix */</span></span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</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;">prefix_len</span><span class="p">)</span> <span class="p">{</span></span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="c"> <span class="n" style="color: #333;">prefix</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;">prefix</span><span class="p">;</span></span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="c"> <span class="n" style="color: #333;">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;">prefix_len</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="73" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="c"> <span class="n" style="color: #333;">Prefix</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="74" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="c"> <span class="k" style="font-weight: 600;">while</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">--</span><span class="p">)</span> <span class="p">{</span></span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="c"> <span class="n" style="color: #333;">Prefix</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;">bases</span><span class="p">[</span><span class="n" style="color: #333;">prefix</span> <span class="o" style="font-weight: 600;">&</span> <span class="mi" style="color: #099;">3</span><span class="p">];</span></span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="c"> <span class="n" style="color: #333;">prefix</span> <span class="o" style="font-weight: 600;">>>=</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span></span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="c"> <span class="p">}</span></span>
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78
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<pre style="margin: 0;">+<span id="LC78" 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;">"prefix:</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%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;">Prefix</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="79" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
79
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<pre style="margin: 0;">+<span id="LC79" 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;">templates</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">prefix</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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80
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<pre style="margin: 0;">+<span id="LC80" 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;">"prefix:</span><span class="se" style="color: #d14;">\t</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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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="82" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="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;">"# uniq k-mers:</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%lu</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;">templates</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">n</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="83" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="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;">"k-mer fraqtion covered:</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%f</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;">templates</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">power</span><span class="p">(</span><span class="mi" style="color: #099;">4</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;">kmersize</span><span class="p">));</span></span>
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<td class="diff-line-num new new_line" data-linenumber="84" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="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;">"inferred tax size:</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%lu</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;">templates</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">v_index</span><span class="p">);</span></span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="c"> </span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* get number of unique inferred tax */</span></span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="c"> <span class="n" style="color: #333;">ntax</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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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="c"> <span class="n" style="color: #333;">v_index</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;">v_index</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</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="n" style="color: #333;">USHRT_MAX</span><span class="p">)</span> <span class="p">{</span></span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="c"> <span class="n" style="color: #333;">values_s</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;">values_s</span><span class="p">;</span></span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="c"> <span class="k" style="font-weight: 600;">while</span><span class="p">(</span><span class="n" style="color: #333;">v_index</span><span class="p">)</span> <span class="p">{</span></span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="c"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">ntax</span><span class="p">;</span></span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="c"> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">values_s</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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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="c"> <span class="n" style="color: #333;">v_index</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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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="c"> <span class="n" style="color: #333;">values_s</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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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="c"> <span class="p">}</span></span>
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97
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<pre style="margin: 0;">+<span id="LC97" 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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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="c"> <span class="n" style="color: #333;">values</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;">values</span><span class="p">;</span></span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="c"> <span class="k" style="font-weight: 600;">while</span><span class="p">(</span><span class="n" style="color: #333;">v_index</span><span class="p">)</span> <span class="p">{</span></span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="c"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">ntax</span><span class="p">;</span></span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="c"> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">values</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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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="c"> <span class="n" style="color: #333;">v_index</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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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="c"> <span class="n" style="color: #333;">values</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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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="c"> <span class="p">}</span></span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="c"> <span class="p">}</span></span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"# inferred taxids:</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%lu</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;">ntax</span><span class="p">);</span></span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="c"> </span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* get min, max, mean and variance of k-mer uniqueness */</span></span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</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;">size</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;">templates</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">mask</span><span class="p">)</span> <span class="p">{</span></span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</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;">v_index</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">UINT_MAX</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="c"> <span class="n" style="color: #333;">value_index</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;">exist</span><span class="p">;</span></span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="c"> <span class="n" style="color: #333;">value_index_l</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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113
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<pre style="margin: 0;">+<span id="LC113" 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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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="c"> <span class="n" style="color: #333;">value_index</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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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="c"> <span class="n" style="color: #333;">value_index_l</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;">exist_l</span><span class="p">;</span></span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="c"> <span class="p">}</span></span>
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117
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<pre style="margin: 0;">+<span id="LC117" 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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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</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;">n</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">UINT_MAX</span><span class="p">)</span> <span class="p">{</span></span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="c"> <span class="n" style="color: #333;">value_index</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;">value_index</span><span class="p">;</span></span>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="c"> <span class="n" style="color: #333;">value_index_l</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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121
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<pre style="margin: 0;">+<span id="LC121" 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="LC122" class="line" lang="c"> <span class="n" style="color: #333;">value_index</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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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="c"> <span class="n" style="color: #333;">value_index_l</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;">value_index_l</span><span class="p">;</span></span>
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124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="c"> <span class="p">}</span></span>
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125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="c"> <span class="p">}</span></span>
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126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</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="n" style="color: #333;">USHRT_MAX</span><span class="p">)</span> <span class="p">{</span></span>
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127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="c"> <span class="n" style="color: #333;">values</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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128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="c"> <span class="n" style="color: #333;">values_s</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;">values_s</span><span class="p">;</span></span>
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129
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<pre style="margin: 0;">+<span id="LC129" 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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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="c"> <span class="n" style="color: #333;">values</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;">values</span><span class="p">;</span></span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="c"> <span class="n" style="color: #333;">values_s</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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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="c"> <span class="p">}</span></span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="c"> <span class="n" style="color: #333;">n</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;">n</span><span class="p">;</span></span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="c"> <span class="n" style="color: #333;">size</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">n</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="135" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="c"> <span class="n" style="color: #333;">min</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>
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<td class="diff-line-num new new_line" data-linenumber="136" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="c"> <span class="n" style="color: #333;">max</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="137" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="c"> <span class="n" style="color: #333;">mean</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="138" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="c"> <span class="n" style="color: #333;">var</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="139" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="c"> <span class="k" style="font-weight: 600;">while</span><span class="p">(</span><span class="n" style="color: #333;">size</span><span class="p">)</span> <span class="p">{</span></span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="c"> <span class="n" style="color: #333;">index</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">value_index</span> <span class="o" style="font-weight: 600;">?</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">value_index</span><span class="o" style="font-weight: 600;">++</span> <span class="o" style="font-weight: 600;">:</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">value_index_l</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">index</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 new new_line" data-linenumber="142" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="c"> <span class="n" style="color: #333;">index</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">values</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">values</span><span class="p">[</span><span class="n" style="color: #333;">index</span><span class="p">]</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">values_s</span><span class="p">[</span><span class="n" style="color: #333;">index</span><span class="p">];</span></span>
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143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">index</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">min</span><span class="p">)</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="n" style="color: #333;">min</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">index</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="p">}</span></span>
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146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">max</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">index</span><span class="p">)</span> <span class="p">{</span></span>
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147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="c"> <span class="n" style="color: #333;">max</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">index</span><span class="p">;</span></span>
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148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="c"> <span class="p">}</span></span>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="c"> <span class="n" style="color: #333;">mean</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">index</span><span class="p">;</span></span>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="c"> </span>
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151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* avoid overflow on var */</span></span>
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152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="c"> <span class="n" style="color: #333;">tmp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">index</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">index</span><span class="p">;</span></span>
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153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="c"> <span class="n" style="color: #333;">tmp</span> <span class="o" style="font-weight: 600;">/=</span> <span class="n" style="color: #333;">n</span><span class="p">;</span></span>
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154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="c"> <span class="n" style="color: #333;">var</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">tmp</span><span class="p">;</span></span>
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="c"> </span>
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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="c"> <span class="o" style="font-weight: 600;">--</span><span class="n" style="color: #333;">size</span><span class="p">;</span></span>
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157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="c"> <span class="p">}</span></span>
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158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="c"> <span class="n" style="color: #333;">mean</span> <span class="o" style="font-weight: 600;">/=</span> <span class="n" style="color: #333;">n</span><span class="p">;</span></span>
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160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="c"> <span class="n" style="color: #333;">var</span> <span class="o" style="font-weight: 600;">-=</span> <span class="n" style="color: #333;">mean</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">mean</span><span class="p">;</span></span>
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161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="c"> </span>
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<td class="diff-line-num new new_line" data-linenumber="162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
162
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<pre style="margin: 0;">+<span id="LC162" 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;">"k-mer co-occurence var:</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%f</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;">var</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="163" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="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;">"k-mer co-occurence mean:</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%f</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;">mean</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="164" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
164
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<pre style="margin: 0;">+<span id="LC164" 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;">"k-mer co-occurence min:</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%d</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;">min</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="165" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
165
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<pre style="margin: 0;">+<span id="LC165" 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;">"k-mer co-occurence max:</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%d</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;">max</span><span class="p">);</span></span>
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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="c"><span class="p">}</span></span>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="c"></span>
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<td class="diff-line-num new new_line" data-linenumber="168" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">helpMessage</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">exeStatus</span><span class="p">)</span> <span class="p">{</span></span>
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">helpOut</span><span class="p">;</span></span>
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170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">exeStatus</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="171" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="c"> <span class="n" style="color: #333;">helpOut</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">stdout</span><span class="p">;</span></span>
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172
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<pre style="margin: 0;">+<span id="LC172" 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 new new_line" data-linenumber="173" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="c"> <span class="n" style="color: #333;">helpOut</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">stderr</span><span class="p">;</span></span>
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174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="c"> <span class="p">}</span></span>
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175
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<pre style="margin: 0;">+<span id="LC175" 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;">"# KMA db gives statistics on a KMA database</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 new_line" data-linenumber="176" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="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;">"# Options are:</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">Desc:</span><span class="se" style="color: #d14;">\t\t\t\t\t</span><span class="s" style="color: #d14;">Requirements:</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 new_line" data-linenumber="177" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
177
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<pre style="margin: 0;">+<span id="LC177" 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;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="178" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
178
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<pre style="margin: 0;">+<span id="LC178" 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;">-t_db</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">Template DB</span><span class="se" style="color: #d14;">\t\t\t\t</span><span class="s" style="color: #d14;">REQUIRED</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 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="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;">-h</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">Shows this help message</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 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="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;">\n</span><span class="s" style="color: #d14;">"</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="n" style="color: #333;">exit</span><span class="p">(</span><span class="n" style="color: #333;">exeStatus</span><span class="p">);</span></span>
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182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="c"><span class="p">}</span></span>
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183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="c"></span>
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<td class="diff-line-num new new_line" data-linenumber="184" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
184
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">db_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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185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="c"> </span>
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186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">args</span><span class="p">;</span></span>
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187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="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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188
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="c"> </span>
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189
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* set defaults */</span></span>
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190
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="c"> <span class="n" style="color: #333;">filename</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="191" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
191
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="c"> <span class="n" style="color: #333;">args</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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192
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="c"> <span class="k" style="font-weight: 600;">while</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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<td class="diff-line-num new new_line" data-linenumber="193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
193
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="c"> <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;">"-t_db"</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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194
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<pre style="margin: 0;">+<span id="LC194" 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;">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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<td class="diff-line-num new new_line" data-linenumber="195" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
195
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="c"> <span class="n" style="color: #333;">filename</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;">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="mi" style="color: #099;">64</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="196" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
196
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="c"> <span class="n" style="color: #333;">strcpy</span><span class="p">(</span><span class="n" style="color: #333;">filename</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>
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<td class="diff-line-num new new_line" data-linenumber="197" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
197
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="198" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
198
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<pre style="margin: 0;">+<span id="LC198" 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;">"-h"</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="199" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
199
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="c"> <span class="n" style="color: #333;">helpMessage</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 new new_line" data-linenumber="200" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
200
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<pre style="margin: 0;">+<span id="LC200" 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 new new_line" data-linenumber="201" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
201
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="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 option:</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%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;">argv</span><span class="p">[</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="202" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
202
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<pre style="margin: 0;">+<span id="LC202" 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;">" Printing help message:</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 new_line" data-linenumber="203" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
203
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="c"> <span class="n" style="color: #333;">helpMessage</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="204" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
204
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="205" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
205
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<pre style="margin: 0;">+<span id="LC205" 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="206" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
206
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="207" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
207
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="c"> </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="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;">filename</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="209" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
209
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<pre style="margin: 0;">+<span id="LC209" 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;">"Insuffient amount of arguments handed!!!</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 new_line" data-linenumber="210" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
210
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="c"> <span class="n" style="color: #333;">helpMessage</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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211
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="c"> <span class="p">}</span></span>
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212
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="c"> </span>
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213
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="c"> <span class="n" style="color: #333;">dbInfo</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="p">);</span></span>
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214
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="c"> </span>
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215
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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216
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="c"><span class="p">}</span></span></pre>
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<a href="https://salsa.debian.org/med-team/kma/-/commit/5f0f33279035adaa9d300bd1041d8fbff645219b#c6094033a6a88ccec0d79878461e205d3414e446"><strong>db.h</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/* Philip T.L.C. Clausen Jan 2017 plan@dtu.dk */</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/*</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * Copyright (c) 2017, Philip Clausen, Technical University of Denmark</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * All rights reserved.</span></span>
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<pre style="margin: 0;">+<span id="LC6" 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="LC7" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * Licensed under the Apache License, Version 2.0 (the "License");</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * you may not use this file except in compliance with the License.</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * You may obtain a copy of the License at</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * http://www.apache.org/licenses/LICENSE-2.0</span></span>
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<pre style="margin: 0;">+<span id="LC12" 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="LC13" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * Unless required by applicable law or agreed to in writing, software</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * distributed under the License is distributed on an "AS IS" BASIS,</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * See the License for the specific language governing permissions and</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * 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="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">dbInfo</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;">filename</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">db_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></pre>
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<a href="https://salsa.debian.org/med-team/kma/-/commit/5f0f33279035adaa9d300bd1041d8fbff645219b#5bb411548ec4b39482e6de83d3ad98f29b1162b1"><strong>kma.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">@@ -123,11 +123,12 @@ static void helpMessage(int exeStatus) {</td>
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<pre style="margin: 0;"> <span id="LC123" 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;">-vcf</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">Make vcf file, 2 to apply FT</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">False/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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<pre style="margin: 0;"> <span id="LC124" 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;">-sam</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">Output sam to stdout, 4 to </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;">only output mapped reads, </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;">2096 for aligned</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">False/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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125
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<td class="diff-line-num new_line" data-linenumber="125" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
125
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<pre style="margin: 0;"> <span id="LC125" 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;">-nc</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">No consensus file</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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<td class="diff-line-num new old_line" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="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;">-na</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">No aln file</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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<td class="diff-line-num old_line" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
126
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<td class="diff-line-num new_line" data-linenumber="127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
127
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<pre style="margin: 0;"> <span id="LC127" 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;">-nf</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">No frag file</span><span class="se" style="color: #d14;">\t\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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<td class="diff-line-num old_line" data-linenumber="127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
127
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<td class="diff-line-num new_line" data-linenumber="128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
128
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<pre style="margin: 0;"> <span id="LC128" 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;">-deCon</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">Remove contamination</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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<td class="diff-line-num old_line" data-linenumber="128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
128
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<td class="diff-line-num new_line" data-linenumber="129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
129
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<pre style="margin: 0;"> <span id="LC129" class="line" lang="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;">-dense</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">Do not allow insertions</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;">in assembly</span><span class="se" style="color: #d14;">\t\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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<td class="diff-line-num old_line" data-linenumber="129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
129
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<td class="diff-line-num new_line" data-linenumber="130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
130
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<pre style="margin: 0;"> <span id="LC130" class="line" lang="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;">-sasm</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">Skip alignment and assembly</span><span class="se" style="color: #d14;">\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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130
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<td class="diff-line-num new_line old" data-linenumber="131" style="width: 35px; color: rgba(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="LC130" 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;">-ref_fsa</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">Consensus sequnce will</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;">have </span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">n</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;"> instead of gaps</span><span class="se" style="color: #d14;">\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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<td class="diff-line-num new old_line" data-linenumber="131" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="131" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="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;">-ref_fsa</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">Consensus sequnce will</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;">have </span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">n</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;"> instead of gaps</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">False<span class="idiff left right"> / 0</span></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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131
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<td class="diff-line-num new_line" data-linenumber="132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
132
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<pre style="margin: 0;"> <span id="LC132" class="line" lang="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;">-matrix</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">Print assembly matrix</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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132
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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;">-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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133
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<td class="diff-line-num new_line" data-linenumber="134" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
134
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<pre style="margin: 0;"> <span id="LC134" class="line" lang="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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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="162" style="width: 35px; color: rgba(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="163" style="width: 35px; color: rgba(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">@@ -162,7 +163,7 @@ static void helpMessage(int exeStatus) {</td>
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162
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<td class="diff-line-num new_line" data-linenumber="163" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
163
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<pre style="margin: 0;"> <span id="LC163" 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;">-gapopen</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">Penalty for gap opening</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">-3</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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163
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<td class="diff-line-num new_line" data-linenumber="164" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
164
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<pre style="margin: 0;"> <span id="LC164" 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;">-gapextend</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">Penalty for gap extension</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">-1</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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164
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<td class="diff-line-num new_line" data-linenumber="165" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
165
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<pre style="margin: 0;"> <span id="LC165" 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;">-per</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">Reward for pairing reads</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">7</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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165
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<pre style="margin: 0;">-<span id="LC165" 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;">-localopen</span><span class="se" style="color: #d14;">\t<span class="idiff left right">\t</span></span><span class="s" style="color: #d14;">Penalty for openning a local chain</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">-6</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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166
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<pre style="margin: 0;">+<span id="LC166" 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;">-localopen</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">Penalty for openning a local chain</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">-6</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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166
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167
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<pre style="margin: 0;"> <span id="LC167" 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;">-Npenalty</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">Penalty matching N</span><span class="se" style="color: #d14;">\t\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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167
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168
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<pre style="margin: 0;"> <span id="LC168" 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;">-transition</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">Penalty for transition</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">-2</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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168
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169
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<pre style="margin: 0;"> <span id="LC169" 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;">-transversion</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">Penalty for transversion</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">-2</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="535" style="width: 35px; color: rgba(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="536" style="width: 35px; color: rgba(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">@@ -535,6 +536,17 @@ int kma_main(int argc, char *argv[]) {</td>
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535
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536
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<pre style="margin: 0;"> <span id="LC536" class="line" lang="c"> <span class="n" style="color: #333;">print_all</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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536
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<td class="diff-line-num new_line" data-linenumber="537" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
537
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<pre style="margin: 0;"> <span id="LC537" 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;">"-ref_fsa"</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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537
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538
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<pre style="margin: 0;"> <span id="LC538" class="line" lang="c"> <span class="n" style="color: #333;">ref_fsa</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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539
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<pre style="margin: 0;">+<span id="LC539" 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;">args</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">argc</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">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="sc" style="color: #d14;">'-'</span><span class="p">)</span> <span class="p">{</span></span>
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540
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<pre style="margin: 0;">+<span id="LC540" class="line" lang="c"> <span class="n" style="color: #333;">ref_fsa</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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<td class="diff-line-num new new_line" data-linenumber="541" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
541
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<pre style="margin: 0;">+<span id="LC541" 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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542
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<pre style="margin: 0;">+<span id="LC542" 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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543
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<pre style="margin: 0;">+<span id="LC543" 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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544
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<pre style="margin: 0;">+<span id="LC544" 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;">ref_fsa</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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545
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<pre style="margin: 0;">+<span id="LC545" class="line" lang="c"> <span class="n" style="color: #333;">ref_fsa</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span></span>
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546
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<pre style="margin: 0;">+<span id="LC546" class="line" lang="c"> <span class="p">}</span></span>
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547
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<pre style="margin: 0;">+<span id="LC547" 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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548
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<pre style="margin: 0;">+<span id="LC548" 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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549
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<pre style="margin: 0;">+<span id="LC549" class="line" lang="c"> <span class="p">}</span></span>
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538
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<td class="diff-line-num new_line" data-linenumber="550" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
550
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<pre style="margin: 0;"> <span id="LC550" 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;">"-Sparse"</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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539
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551
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<pre style="margin: 0;"> <span id="LC551" 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;">1</span><span class="p">;</span></span>
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540
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<td class="diff-line-num new_line" data-linenumber="552" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
552
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<pre style="margin: 0;"> <span id="LC552" 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;">"-1t1"</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="551" style="width: 35px; color: rgba(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="563" style="width: 35px; color: rgba(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">@@ -551,7 +563,7 @@ int kma_main(int argc, char *argv[]) {</td>
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551
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563
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<pre style="margin: 0;"> <span id="LC563" 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="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">support</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">||</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">support</span><span class="p">)</span> <span class="p">{</span></span>
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552
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564
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<pre style="margin: 0;"> <span id="LC564" 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;">-proxi</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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553
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565
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<pre style="margin: 0;"> <span id="LC565" class="line" lang="c"> <span class="n" style="color: #333;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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554
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<pre style="margin: 0;">-<span id="LC554" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;"><span class="idiff left">if</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">support</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">!=</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff right">)</span></span> <span class="p">{</span></span>
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566
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<pre style="margin: 0;">+<span id="LC566" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;"><span class="idiff left right">else</span></span> <span class="p">{</span></span>
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555
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567
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<pre style="margin: 0;"> <span id="LC567" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* set proximity parameter */</span></span>
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556
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568
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<pre style="margin: 0;"> <span id="LC568" class="line" lang="c"> <span class="n" style="color: #333;">getMatch</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">getProxiMatch</span><span class="p">;</span></span>
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557
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569
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<pre style="margin: 0;"> <span id="LC569" class="line" lang="c"> <span class="n" style="color: #333;">getMatchSparse</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">getProxiMatchSparse</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="815" style="width: 35px; color: rgba(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="827" style="width: 35px; color: rgba(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">@@ -815,6 +827,8 @@ int kma_main(int argc, char *argv[]) {</td>
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815
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827
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<pre style="margin: 0;"> <span id="LC827" class="line" lang="c"> <span class="p">}</span></span>
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816
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<td class="diff-line-num new_line" data-linenumber="828" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
828
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<pre style="margin: 0;"> <span id="LC828" 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;">"-nc"</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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817
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<td class="diff-line-num new_line" data-linenumber="829" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
829
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<pre style="margin: 0;"> <span id="LC829" 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;">1</span><span class="p">;</span></span>
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<td class="diff-line-num new old_line" data-linenumber="818" style="width: 35px; color: rgba(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="830" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
830
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<pre style="margin: 0;">+<span id="LC830" 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;">"-na"</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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831
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<pre style="margin: 0;">+<span id="LC831" 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;">2</span><span class="p">;</span></span>
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818
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832
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<pre style="margin: 0;"> <span id="LC832" 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;">"-nf"</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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833
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<pre style="margin: 0;"> <span id="LC833" class="line" lang="c"> <span class="n" style="color: #333;">nf</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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820
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834
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<pre style="margin: 0;"> <span id="LC834" 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;">"-cge"</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="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -886,7 +900,7 @@ int kma_main(int argc, char *argv[]) {</td>
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886
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900
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<pre style="margin: 0;"> <span id="LC900" class="line" lang="c"> <span class="p">}</span></span>
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887
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901
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<pre style="margin: 0;"> <span id="LC901" class="line" lang="c"> <span class="p">}</span></span>
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888
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902
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<pre style="margin: 0;"> <span id="LC902" class="line" lang="c"> </span>
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889
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<pre style="margin: 0;">-<span id="LC889" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">ref_fsa</span><span class="p">)</span> <span class="p">{</span></span>
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903
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<pre style="margin: 0;">+<span id="LC903" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">ref_fsa</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">1</span></span><span class="p">)</span> <span class="p">{</span></span>
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890
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904
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<pre style="margin: 0;"> <span id="LC904" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">baseCall</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">nanoCaller</span><span class="p">)</span> <span class="p">{</span></span>
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891
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905
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<pre style="margin: 0;"> <span id="LC905" class="line" lang="c"> <span class="n" style="color: #333;">baseCall</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">refNanoCaller</span><span class="p">;</span></span>
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892
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906
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<pre style="margin: 0;"> <span id="LC906" 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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<li id="406e031b8824ea26ae0bf4d7579a1d89e3fb5906">
<a href="https://salsa.debian.org/med-team/kma/-/commit/5f0f33279035adaa9d300bd1041d8fbff645219b#406e031b8824ea26ae0bf4d7579a1d89e3fb5906"><strong>main.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">@@ -18,6 +18,7 @@</td>
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18
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18
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">*/</span></span>
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19
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19
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define _XOPEN_SOURCE 600</span></span>
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20
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20
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <string.h></span></span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "db.h"</span></span>
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21
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22
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "dist.h"</span></span>
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22
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23
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "kma.h"</span></span>
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24
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "index.h"</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -34,6 +35,7 @@ static int helpmessage(FILE *out) {</td>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="s" style="color: #d14;">"# %16s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%-32s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="s" style="color: #d14;">"shm"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Shared memory"</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="s" style="color: #d14;">"# %16s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%-32s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="s" style="color: #d14;">"seq2fasta"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Conversion of database to fasta"</span><span class="p">);</span></span>
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36
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37
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="s" style="color: #d14;">"# %16s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%-32s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="s" style="color: #d14;">"dist"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Calculate distance measures between templates"</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="s" style="color: #d14;">"# %16s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%-32s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="s" style="color: #d14;">"db"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Make statistics on KMA db"</span><span class="p">);</span></span>
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37
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<td class="diff-line-num new_line" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
39
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="s" style="color: #d14;">"# %16s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%-32s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="s" style="color: #d14;">"update"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Update database to current version"</span><span class="p">);</span></span>
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38
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<td class="diff-line-num new_line" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
40
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="s" style="color: #d14;">"# %16s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%-32s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="s" style="color: #d14;">"-c"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Citation"</span><span class="p">);</span></span>
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39
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<td class="diff-line-num new_line" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
41
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="s" style="color: #d14;">"# %16s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%-32s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="s" style="color: #d14;">"-v"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Version"</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="58" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="60" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -58,6 +60,8 @@ int main(int argc, char *argv[]) {</td>
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58
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<td class="diff-line-num new_line" data-linenumber="60" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
60
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<pre style="margin: 0;"> <span id="LC60" 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;">dist_main</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>
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<td class="diff-line-num old_line" data-linenumber="59" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
59
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<td class="diff-line-num new_line" data-linenumber="61" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
61
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<pre style="margin: 0;"> <span id="LC61" 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="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">argv</span><span class="p">,</span> <span class="s" style="color: #d14;">"update"</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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60
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<td class="diff-line-num new_line" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
62
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<pre style="margin: 0;"> <span id="LC62" 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;">update_main</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>
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<td class="diff-line-num new new_line" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
63
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<pre style="margin: 0;">+<span id="LC63" 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="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">argv</span><span class="p">,</span> <span class="s" style="color: #d14;">"db"</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="64" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
64
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<pre style="margin: 0;">+<span id="LC64" 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;">db_main</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>
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61
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<td class="diff-line-num new_line" data-linenumber="65" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
65
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<pre style="margin: 0;"> <span id="LC65" 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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62
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<td class="diff-line-num new_line" data-linenumber="66" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
66
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<pre style="margin: 0;"> <span id="LC66" 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 option:</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">argv</span><span class="p">);</span></span>
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63
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67
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<pre style="margin: 0;"> <span id="LC67" 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;">helpmessage</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">);</span></span>
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<a href="https://salsa.debian.org/med-team/kma/-/commit/5f0f33279035adaa9d300bd1041d8fbff645219b#088a2f1aaa170cd721dbae6f4b2bcb8239c7119a"><strong>mt1.c</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="135" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -135,6 +135,11 @@ void runKMA_Mt1(char *templatefilename, char *outputfilename, char *exePrev, int</td>
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135
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135
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<pre style="margin: 0;"> <span id="LC135" class="line" lang="c"> <span class="n" style="color: #333;">strcat</span><span class="p">(</span><span class="n" style="color: #333;">outputfilename</span><span class="p">,</span> <span class="s" style="color: #d14;">".fsa"</span><span class="p">);</span></span>
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<td class="diff-line-num old_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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136
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<pre style="margin: 0;"> <span id="LC136" class="line" lang="c"> <span class="n" style="color: #333;">consensus_out</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sfopen</span><span class="p">(</span><span class="n" style="color: #333;">outputfilename</span><span class="p">,</span> <span class="s" style="color: #d14;">"w"</span><span class="p">);</span></span>
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137
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137
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<pre style="margin: 0;"> <span id="LC137" class="line" lang="c"> <span class="n" style="color: #333;">outputfilename</span><span class="p">[</span><span class="n" style="color: #333;">file_len</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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138
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<pre style="margin: 0;">+<span id="LC138" 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;">nc</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">2</span><span class="p">)</span> <span class="p">{</span></span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="c"> <span class="n" style="color: #333;">alignment_out</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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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="c"> <span class="n" style="color: #333;">strcat</span><span class="p">(</span><span class="n" style="color: #333;">outputfilename</span><span class="p">,</span> <span class="s" style="color: #d14;">".fsa"</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="c"> <span class="n" style="color: #333;">consensus_out</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sfopen</span><span class="p">(</span><span class="n" style="color: #333;">outputfilename</span><span class="p">,</span> <span class="s" style="color: #d14;">"w"</span><span class="p">);</span></span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="c"> <span class="n" style="color: #333;">outputfilename</span><span class="p">[</span><span class="n" style="color: #333;">file_len</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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138
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143
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<pre style="margin: 0;"> <span id="LC143" 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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139
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<pre style="margin: 0;"> <span id="LC144" class="line" lang="c"> <span class="n" style="color: #333;">alignment_out</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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140
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145
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<pre style="margin: 0;"> <span id="LC145" class="line" lang="c"> <span class="n" style="color: #333;">consensus_out</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 new_line" data-linenumber="417" style="width: 35px; color: rgba(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">@@ -412,7 +417,7 @@ void runKMA_Mt1(char *templatefilename, char *outputfilename, char *exePrev, int</td>
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412
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417
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<pre style="margin: 0;"> <span id="LC417" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Output result */</span></span>
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413
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418
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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;">res_out</span><span class="p">,</span> <span class="s" style="color: #d14;">"%-12s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%8lu</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%8d</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%8d</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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414
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419
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<pre style="margin: 0;"> <span id="LC419" class="line" lang="c"> <span class="kr" style="font-weight: 600;">thread</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">template_name</span><span class="p">,</span> <span class="n" style="color: #333;">read_score</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">t_len</span><span class="p">,</span> <span class="n" style="color: #333;">id</span><span class="p">,</span> <span class="n" style="color: #333;">cover</span><span class="p">,</span> <span class="n" style="color: #333;">q_id</span><span class="p">,</span> <span class="n" style="color: #333;">q_cover</span><span class="p">,</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)</span> <span class="n" style="color: #333;">depth</span><span class="p">,</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)</span> <span class="n" style="color: #333;">read_score</span><span class="p">,</span> <span class="n" style="color: #333;">p_value</span><span class="p">);</span></span>
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415
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<pre style="margin: 0;">-<span id="LC415" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">nc</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">0</span></span><span class="p">)</span> <span class="p">{</span></span>
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420
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<pre style="margin: 0;">+<span id="LC420" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">nc</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 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;">printConsensus</span><span class="p">(</span><span class="n" style="color: #333;">aligned_assem</span><span class="p">,</span> <span class="kr" style="font-weight: 600;">thread</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">template_name</span><span class="p">,</span> <span class="n" style="color: #333;">alignment_out</span><span class="p">,</span> <span class="n" style="color: #333;">consensus_out</span><span class="p">,</span> <span class="n" style="color: #333;">ref_fsa</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC422" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC423" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* print matrix */</span></span>
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<a href="https://salsa.debian.org/med-team/kma/-/commit/5f0f33279035adaa9d300bd1041d8fbff645219b#76d4a085858e48da0f768edd95269019d42998c9"><strong>printconsensus.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">@@ -27,21 +27,16 @@ void printConsensus(Assem *aligned_assem, char *header, FILE *alignment_out, FIL</td>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* print alignment */</span></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="c"> <span class="n" style="color: #333;">aln_len</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">aligned_assem</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">len</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">alignment_out</span><span class="p">,</span> <span class="s" style="color: #d14;">"# %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;">header</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC31" 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;">aln_len</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;">60</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 class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">alignment_out</span><span class="p">,</span> <span class="s" style="color: #d14;">"%-10s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%.60s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="s" style="color: #d14;">"template:"</span><span class="p">,</span> <span class="n" style="color: #333;">aligned_assem</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">t</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">i</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">alignment_out</span><span class="p">,</span> <span class="s" style="color: #d14;">"%-10s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%.60s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="n" style="color: #333;">aligned_assem</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">s</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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<pre style="margin: 0;">-<span id="LC34" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">alignment_out</span><span class="p">,</span> <span class="s" style="color: #d14;">"%-10s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%.60s</span><span class="se" style="color: #d14;">\n\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="s" style="color: #d14;">"query:"</span><span class="p">,</span> <span class="n" style="color: #333;">aligned_assem</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">q</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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<pre style="margin: 0;">+<span id="LC30" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">alignment_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="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">alignment_out</span><span class="p">,</span> <span class="s" style="color: #d14;">"# %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;">header</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC32" 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;">aln_len</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;">60</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">alignment_out</span><span class="p">,</span> <span class="s" style="color: #d14;">"%-10s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%.60s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="s" style="color: #d14;">"template:"</span><span class="p">,</span> <span class="n" style="color: #333;">aligned_assem</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">t</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">i</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">alignment_out</span><span class="p">,</span> <span class="s" style="color: #d14;">"%-10s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%.60s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="n" style="color: #333;">aligned_assem</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">s</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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<pre style="margin: 0;">+<span id="LC35" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">alignment_out</span><span class="p">,</span> <span class="s" style="color: #d14;">"%-10s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%.60s</span><span class="se" style="color: #d14;">\n\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="s" style="color: #d14;">"query:"</span><span class="p">,</span> <span class="n" style="color: #333;">aligned_assem</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">q</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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<pre style="margin: 0;">+<span id="LC36" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Prepare consensus */</span></span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">ref_fsa</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;">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;">aln_len</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="LC40" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">aligned_assem</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">q</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'-'</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="c"> <span class="n" style="color: #333;">aligned_assem</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">q</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="sc" style="color: #d14;">'n'</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC44" 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="LC39" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">ref_fsa</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC40" 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;">bias</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;">aln_len</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">bias</span><span class="p">)</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;">aligned_assem</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">q</span><span class="p">[</span><span class="n" style="color: #333;">bias</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">aligned_assem</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">q</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">aligned_assem</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">q</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'-'</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -50,7 +45,14 @@ void printConsensus(Assem *aligned_assem, char *header, FILE *alignment_out, FIL</td>
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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;">aln_len</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bias</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="c"> <span class="n" style="color: #333;">aligned_assem</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">q</span><span class="p">[</span><span class="n" style="color: #333;">aln_len</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC48" 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;">ref_fsa</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC49" 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;">aln_len</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="LC50" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">aligned_assem</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">q</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'-'</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="c"> <span class="n" style="color: #333;">aligned_assem</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">q</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="sc" style="color: #d14;">'n'</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 class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="c"> <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="cm" style="color: #998; font-style: italic;">/* Print consensus */</span></span>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">consensus_out</span><span class="p">,</span> <span class="s" style="color: #d14;">">%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;">header</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC58" 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;">aln_len</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;">60</span><span class="p">)</span> <span class="p">{</span></span>
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<a href="https://salsa.debian.org/med-team/kma/-/commit/5f0f33279035adaa9d300bd1041d8fbff645219b#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">@@ -236,6 +236,11 @@ int runKMA(char *templatefilename, char *outputfilename, char *exePrev, int ConC</td>
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<pre style="margin: 0;"> <span id="LC236" class="line" lang="c"> <span class="n" style="color: #333;">strcat</span><span class="p">(</span><span class="n" style="color: #333;">outputfilename</span><span class="p">,</span> <span class="s" style="color: #d14;">".fsa"</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC237" class="line" lang="c"> <span class="n" style="color: #333;">consensus_out</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sfopen</span><span class="p">(</span><span class="n" style="color: #333;">outputfilename</span><span class="p">,</span> <span class="s" style="color: #d14;">"w"</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC238" class="line" lang="c"> <span class="n" style="color: #333;">outputfilename</span><span class="p">[</span><span class="n" style="color: #333;">file_len</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC239" 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;">nc</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">2</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC240" class="line" lang="c"> <span class="n" style="color: #333;">alignment_out</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="LC241" class="line" lang="c"> <span class="n" style="color: #333;">strcat</span><span class="p">(</span><span class="n" style="color: #333;">outputfilename</span><span class="p">,</span> <span class="s" style="color: #d14;">".fsa"</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC242" class="line" lang="c"> <span class="n" style="color: #333;">consensus_out</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sfopen</span><span class="p">(</span><span class="n" style="color: #333;">outputfilename</span><span class="p">,</span> <span class="s" style="color: #d14;">"w"</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC243" class="line" lang="c"> <span class="n" style="color: #333;">outputfilename</span><span class="p">[</span><span class="n" style="color: #333;">file_len</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC244" 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="LC245" class="line" lang="c"> <span class="n" style="color: #333;">alignment_out</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="LC246" class="line" lang="c"> <span class="n" style="color: #333;">consensus_out</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="1234" style="width: 35px; color: rgba(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="1239" style="width: 35px; color: rgba(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">@@ -1234,7 +1239,7 @@ int runKMA(char *templatefilename, char *outputfilename, char *exePrev, int ConC</td>
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1234
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1239
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<pre style="margin: 0;"> <span id="LC1239" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Output result */</span></span>
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1235
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1240
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<pre style="margin: 0;"> <span id="LC1240" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">res_out</span><span class="p">,</span> <span class="s" style="color: #d14;">"%-12s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%8ld</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%8u</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%8d</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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1241
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<pre style="margin: 0;"> <span id="LC1241" class="line" lang="c"> <span class="kr" style="font-weight: 600;">thread</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">template_name</span><span class="p">,</span> <span class="n" style="color: #333;">read_score</span><span class="p">,</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span><span class="p">)</span> <span class="n" style="color: #333;">expected</span><span class="p">,</span> <span class="n" style="color: #333;">t_len</span><span class="p">,</span> <span class="n" style="color: #333;">id</span><span class="p">,</span> <span class="n" style="color: #333;">cover</span><span class="p">,</span> <span class="n" style="color: #333;">q_id</span><span class="p">,</span> <span class="n" style="color: #333;">q_cover</span><span class="p">,</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)</span> <span class="n" style="color: #333;">depth</span><span class="p">,</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)</span> <span class="n" style="color: #333;">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="LC1237" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">nc</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">0</span></span><span class="p">)</span> <span class="p">{</span></span>
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1242
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<pre style="margin: 0;">+<span id="LC1242" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">nc</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 class="p">{</span></span>
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1238
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1243
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<pre style="margin: 0;"> <span id="LC1243" class="line" lang="c"> <span class="n" style="color: #333;">printConsensus</span><span class="p">(</span><span class="n" style="color: #333;">aligned_assem</span><span class="p">,</span> <span class="kr" style="font-weight: 600;">thread</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">template_name</span><span class="p">,</span> <span class="n" style="color: #333;">alignment_out</span><span class="p">,</span> <span class="n" style="color: #333;">consensus_out</span><span class="p">,</span> <span class="n" style="color: #333;">ref_fsa</span><span class="p">);</span></span>
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1239
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1244
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<pre style="margin: 0;"> <span id="LC1244" class="line" lang="c"> <span class="p">}</span></span>
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1240
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1245
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<pre style="margin: 0;"> <span id="LC1245" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* print matrix */</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1429" style="width: 35px; color: rgba(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="1434" style="width: 35px; color: rgba(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">@@ -1429,6 +1434,11 @@ int runKMA_MEM(char *templatefilename, char *outputfilename, char *exePrev, int</td>
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1429
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1434
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<pre style="margin: 0;"> <span id="LC1434" class="line" lang="c"> <span class="n" style="color: #333;">strcat</span><span class="p">(</span><span class="n" style="color: #333;">outputfilename</span><span class="p">,</span> <span class="s" style="color: #d14;">".fsa"</span><span class="p">);</span></span>
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1430
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1435
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<pre style="margin: 0;"> <span id="LC1435" class="line" lang="c"> <span class="n" style="color: #333;">consensus_out</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sfopen</span><span class="p">(</span><span class="n" style="color: #333;">outputfilename</span><span class="p">,</span> <span class="s" style="color: #d14;">"w"</span><span class="p">);</span></span>
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1431
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1436
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<pre style="margin: 0;"> <span id="LC1436" class="line" lang="c"> <span class="n" style="color: #333;">outputfilename</span><span class="p">[</span><span class="n" style="color: #333;">file_len</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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1437
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<pre style="margin: 0;">+<span id="LC1437" 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;">nc</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">2</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC1438" class="line" lang="c"> <span class="n" style="color: #333;">alignment_out</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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1439
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<pre style="margin: 0;">+<span id="LC1439" class="line" lang="c"> <span class="n" style="color: #333;">strcat</span><span class="p">(</span><span class="n" style="color: #333;">outputfilename</span><span class="p">,</span> <span class="s" style="color: #d14;">".fsa"</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC1440" class="line" lang="c"> <span class="n" style="color: #333;">consensus_out</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sfopen</span><span class="p">(</span><span class="n" style="color: #333;">outputfilename</span><span class="p">,</span> <span class="s" style="color: #d14;">"w"</span><span class="p">);</span></span>
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1441
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<pre style="margin: 0;">+<span id="LC1441" class="line" lang="c"> <span class="n" style="color: #333;">outputfilename</span><span class="p">[</span><span class="n" style="color: #333;">file_len</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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1432
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1442
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<pre style="margin: 0;"> <span id="LC1442" 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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1433
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1443
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<pre style="margin: 0;"> <span id="LC1443" class="line" lang="c"> <span class="n" style="color: #333;">alignment_out</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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1434
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1444
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<pre style="margin: 0;"> <span id="LC1444" class="line" lang="c"> <span class="n" style="color: #333;">consensus_out</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 new_line" data-linenumber="2396" style="width: 35px; color: rgba(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">@@ -2386,7 +2396,7 @@ int runKMA_MEM(char *templatefilename, char *outputfilename, char *exePrev, int</td>
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2386
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2396
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<pre style="margin: 0;"> <span id="LC2396" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Output result */</span></span>
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2387
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2397
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<pre style="margin: 0;"> <span id="LC2397" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">res_out</span><span class="p">,</span> <span class="s" style="color: #d14;">"%-12s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%8ld</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%8u</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%8d</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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2388
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2398
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<pre style="margin: 0;"> <span id="LC2398" class="line" lang="c"> <span class="kr" style="font-weight: 600;">thread</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">template_name</span><span class="p">,</span> <span class="n" style="color: #333;">read_score</span><span class="p">,</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span><span class="p">)</span> <span class="n" style="color: #333;">expected</span><span class="p">,</span> <span class="n" style="color: #333;">t_len</span><span class="p">,</span> <span class="n" style="color: #333;">id</span><span class="p">,</span> <span class="n" style="color: #333;">cover</span><span class="p">,</span> <span class="n" style="color: #333;">q_id</span><span class="p">,</span> <span class="n" style="color: #333;">q_cover</span><span class="p">,</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)</span> <span class="n" style="color: #333;">depth</span><span class="p">,</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)</span> <span class="n" style="color: #333;">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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2389
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<pre style="margin: 0;">-<span id="LC2389" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">nc</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">0</span></span><span class="p">)</span> <span class="p">{</span></span>
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2399
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<pre style="margin: 0;">+<span id="LC2399" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">nc</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 class="p">{</span></span>
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2390
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2400
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<pre style="margin: 0;"> <span id="LC2400" class="line" lang="c"> <span class="n" style="color: #333;">printConsensus</span><span class="p">(</span><span class="n" style="color: #333;">aligned_assem</span><span class="p">,</span> <span class="kr" style="font-weight: 600;">thread</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">template_name</span><span class="p">,</span> <span class="n" style="color: #333;">alignment_out</span><span class="p">,</span> <span class="n" style="color: #333;">consensus_out</span><span class="p">,</span> <span class="n" style="color: #333;">ref_fsa</span><span class="p">);</span></span>
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2391
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2401
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<pre style="margin: 0;"> <span id="LC2401" class="line" lang="c"> <span class="p">}</span></span>
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2392
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2402
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<pre style="margin: 0;"> <span id="LC2402" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* print matrix */</span></span>
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<a href="https://salsa.debian.org/med-team/kma/-/commit/5f0f33279035adaa9d300bd1041d8fbff645219b#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">@@ -520,6 +520,11 @@ int runKMA_spltDB(char **templatefilenames, int targetNum, char *outputfilename,</td>
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<pre style="margin: 0;"> <span id="LC520" class="line" lang="c"> <span class="n" style="color: #333;">strcat</span><span class="p">(</span><span class="n" style="color: #333;">outputfilename</span><span class="p">,</span> <span class="s" style="color: #d14;">".fsa"</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;">consensus_out</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sfopen</span><span class="p">(</span><span class="n" style="color: #333;">outputfilename</span><span class="p">,</span> <span class="s" style="color: #d14;">"w"</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="n" style="color: #333;">outputfilename</span><span class="p">[</span><span class="n" style="color: #333;">file_len</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC523" 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;">nc</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">2</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC524" class="line" lang="c"> <span class="n" style="color: #333;">alignment_out</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="LC525" class="line" lang="c"> <span class="n" style="color: #333;">strcat</span><span class="p">(</span><span class="n" style="color: #333;">outputfilename</span><span class="p">,</span> <span class="s" style="color: #d14;">".fsa"</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC526" class="line" lang="c"> <span class="n" style="color: #333;">consensus_out</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sfopen</span><span class="p">(</span><span class="n" style="color: #333;">outputfilename</span><span class="p">,</span> <span class="s" style="color: #d14;">"w"</span><span class="p">);</span></span>
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527
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<pre style="margin: 0;">+<span id="LC527" class="line" lang="c"> <span class="n" style="color: #333;">outputfilename</span><span class="p">[</span><span class="n" style="color: #333;">file_len</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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523
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528
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<pre style="margin: 0;"> <span id="LC528" 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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529
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<pre style="margin: 0;"> <span id="LC529" class="line" lang="c"> <span class="n" style="color: #333;">alignment_out</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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530
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<pre style="margin: 0;"> <span id="LC530" class="line" lang="c"> <span class="n" style="color: #333;">consensus_out</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">@@ -1639,7 +1644,7 @@ int runKMA_spltDB(char **templatefilenames, int targetNum, char *outputfilename,</td>
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<pre style="margin: 0;"> <span id="LC1644" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Output result */</span></span>
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<pre style="margin: 0;"> <span id="LC1645" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">res_out</span><span class="p">,</span> <span class="s" style="color: #d14;">"%-12s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%8ld</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%8u</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%8d</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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<td class="diff-line-num old_line" data-linenumber="1641" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1641
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<td class="diff-line-num new_line" data-linenumber="1646" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1646
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<pre style="margin: 0;"> <span id="LC1646" class="line" lang="c"> <span class="kr" style="font-weight: 600;">thread</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">template_name</span><span class="p">,</span> <span class="n" style="color: #333;">read_score</span><span class="p">,</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span><span class="p">)</span> <span class="n" style="color: #333;">expected</span><span class="p">,</span> <span class="n" style="color: #333;">t_len</span><span class="p">,</span> <span class="n" style="color: #333;">id</span><span class="p">,</span> <span class="n" style="color: #333;">cover</span><span class="p">,</span> <span class="n" style="color: #333;">q_id</span><span class="p">,</span> <span class="n" style="color: #333;">q_cover</span><span class="p">,</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)</span> <span class="n" style="color: #333;">depth</span><span class="p">,</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)</span> <span class="n" style="color: #333;">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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1642
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<pre style="margin: 0;">-<span id="LC1642" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">nc</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">0</span></span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC1647" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">nc</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 class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC1648" class="line" lang="c"> <span class="n" style="color: #333;">printConsensus</span><span class="p">(</span><span class="n" style="color: #333;">aligned_assem</span><span class="p">,</span> <span class="kr" style="font-weight: 600;">thread</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">template_name</span><span class="p">,</span> <span class="n" style="color: #333;">alignment_out</span><span class="p">,</span> <span class="n" style="color: #333;">consensus_out</span><span class="p">,</span> <span class="n" style="color: #333;">ref_fsa</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC1649" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC1650" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* print matrix */</span></span>
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<a href="https://salsa.debian.org/med-team/kma/-/commit/5f0f33279035adaa9d300bd1041d8fbff645219b#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 "1.3.<span class="idiff left right">3</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 "1.3.<span class="idiff left right">4</span>"</span></span></pre>
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