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<h3>
Andreas Tille pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/kma">Debian Med / kma</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/kma/commit/f5137c3d39949889292033da254f861b4981ebbf">f5137c3d</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-08-01T11:50:45Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 1.2.10a</pre>
</li>
</ul>
<h4>19 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#1ff221cada819d34daa6f89593fc3d48f1acc3ce">
KMAspecification.pdf
</a>
</li>
<li class="file-stats">
<a href="#836efb6e25a091dcb4ff8e1dbb2f0be6a5cbf14c">
Makefile
</a>
</li>
<li class="file-stats">
<a href="#ddd34e1789cc70e19fb0e89d73fae8d104ed9c40">
align.c
</a>
</li>
<li class="file-stats">
<a href="#150c159b696c4d2657c933fc25c1f6af0b301fe2">
compress.c
</a>
</li>
<li class="file-stats">
<a href="#6f01b21e666698a62c6dd6fcadb36a64d4bc30d4">
frags.c
</a>
</li>
<li class="file-stats">
<a href="#7eed163ea0757dada23cd667898abf840233da45">
index.c
</a>
</li>
<li class="file-stats">
<a href="#5bb411548ec4b39482e6de83d3ad98f29b1162b1">
kma.c
</a>
</li>
<li class="file-stats">
<a href="#57966272a58cfa0f29a50e15609a883267e2471e">
loadupdate.c
</a>
</li>
<li class="file-stats">
<a href="#9f42ead3b08d7f8ac36940bb98a4415aa62390dd">
loadupdate.h
</a>
</li>
<li class="file-stats">
<a href="#e54b00420aceec6f11948d8c279380a68b99ba52">
makeindex.c
</a>
</li>
<li class="file-stats">
<a href="#ace9d341f8ce5776855494d2885e4a314493ec78">
penalties.h
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</li>
<li class="file-stats">
<a href="#ca9efd475143efe0a1b0464c67f49900d98ca75a">
runkma.c
</a>
</li>
<li class="file-stats">
<a href="#f9ead8e7fb7b1680f786604627e0ac2147f4b7ef">
savekmers.c
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<li class="file-stats">
<a href="#5e9149468b1d12c9eb149b26487ea1dfd176a6de">
savekmers.h
</a>
</li>
<li class="file-stats">
<a href="#7fa02bd1b412f83275abb82df0572b57f1958a70">
seq2fasta.c
</a>
</li>
<li class="file-stats">
<a href="#f80652dda49a7117428c0f92935664fc8cd4e2d1">
spltdb.c
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</li>
<li class="file-stats">
<a href="#1c6375d34d9e418d1139bd146337fb256ac24a2a">
<span class="new-file">
+
tmp.c
</span>
</a>
</li>
<li class="file-stats">
<a href="#b09c88ef20c9c024eb7272d240bf1ef251d38efa">
<span class="new-file">
+
tmp.h
</span>
</a>
</li>
<li class="file-stats">
<a href="#2d1dba06c7f4b4c2f13e05d40a391d5330c68ce4">
version.h
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="1ff221cada819d34daa6f89593fc3d48f1acc3ce">
<a href="https://salsa.debian.org/med-team/kma/commit/f5137c3d39949889292033da254f861b4981ebbf#1ff221cada819d34daa6f89593fc3d48f1acc3ce"><strong>KMAspecification.pdf</strong></a>
<hr>
No preview for this file type
<br>
</li>
<li id="836efb6e25a091dcb4ff8e1dbb2f0be6a5cbf14c">
<a href="https://salsa.debian.org/med-team/kma/commit/f5137c3d39949889292033da254f861b4981ebbf#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 class="nt" style="color: #000080;">-std</span><span class="o" style="font-weight: 600;">=</span>c99</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="diff-line-num new_line old" data-linenumber="2" style="width: 35px; color: rgba(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="LC2" 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 ef.o filebuff.o frags.o hashmap.o hashmapindex.o hashmapkma.o hashmapkmers.o hashtable.o index.o kma.o kmapipe.o kmers.o kmmap.o loadupdate.o makeindex.o mt1.o nw.o pherror.o printconsensus.o qseqs.o qualcheck.o runinput.o runkma.o sam.o savekmers.o seq2fasta.o seqparse.o shm.o sparse.o spltdb.o stdnuc.o stdstat.o update.o updateindex.o updatescores.o valueshash.o vcf.o</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="3" style="width: 35px; color: rgba(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="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC2" 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 ef.o filebuff.o frags.o hashmap.o hashmapindex.o hashmapkma.o hashmapkmers.o hashtable.o index.o kma.o kmapipe.o kmers.o kmmap.o loadupdate.o makeindex.o mt1.o nw.o pherror.o printconsensus.o qseqs.o qualcheck.o runinput.o runkma.o sam.o savekmers.o seq2fasta.o seqparse.o shm.o sparse.o spltdb.o stdnuc.o stdstat.o <span class="idiff left right">tmp.o </span>update.o updateindex.o updatescores.o valueshash.o vcf.o</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="3" style="width: 35px; color: rgba(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="3" style="width: 35px; color: rgba(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="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3" 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>
</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>
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<td class="diff-line-num old_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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<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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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC5" class="line" lang="make"><span class="nl">.c .o</span><span class="o" style="font-weight: 600;">:</span></span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="43" style="width: 35px; color: rgba(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="43" style="width: 35px; color: rgba(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">@@ -43,7 +43,7 @@ hashmapkma.o: hashmapkma.h pherror.h</td>
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<td class="diff-line-num old_line" data-linenumber="43" style="width: 35px; color: rgba(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="43" style="width: 35px; color: rgba(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="LC43" class="line" lang="make"><span class="nl">hashmapkmers.o</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">hashmapkmers.h pherror.h</span></span>
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<td class="diff-line-num old_line" data-linenumber="44" style="width: 35px; color: rgba(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="44" style="width: 35px; color: rgba(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="LC44" class="line" lang="make"><span class="nl">hashtable.o</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">hashtable.h hashmapkma.h hashmapkmers.h pherror.h</span></span>
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<td class="diff-line-num old_line" data-linenumber="45" style="width: 35px; color: rgba(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="45" style="width: 35px; color: rgba(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="LC45" class="line" lang="make"><span class="nl">index.o</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">index.h compress.h decon.h hashmap.h hashmapkma.h loadupdate.h makeindex.h pherror.h stdstat.h version.h</span></span>
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<td class="diff-line-num old old_line" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="diff-line-num new_line old" data-linenumber="46" style="width: 35px; color: rgba(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="LC46" class="line" lang="make"><span class="nl">kma.o</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">kma.h ankers.h assembly.h chain.h hashmapkma.h kmers.h mt1.h penalties.h pherror.h qseqs.h runinput.h runkma.h savekmers.h sparse.h spltdb.h version.h</span></span>
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<td class="diff-line-num new old_line" data-linenumber="47" style="width: 35px; color: rgba(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="46" style="width: 35px; color: rgba(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="LC46" class="line" lang="make"><span class="nl">kma.o</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">kma.h ankers.h assembly.h chain.h hashmapkma.h kmers.h mt1.h penalties.h pherror.h qseqs.h runinput.h runkma.h savekmers.h sparse.h spltdb.h <span class="idiff left right">tmp.h </span>version.h</span></span>
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<td class="diff-line-num old_line" data-linenumber="47" style="width: 35px; color: rgba(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="47" style="width: 35px; color: rgba(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="LC47" class="line" lang="make"><span class="nl">kmapipe.o</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">kmapipe.h pherror.h</span></span>
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<td class="diff-line-num old_line" data-linenumber="48" style="width: 35px; color: rgba(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="LC48" class="line" lang="make"><span class="nl">kmers.o</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">kmers.h ankers.h compdna.h hashmapkma.h kmapipe.h pherror.h qseqs.h savekmers.h spltdb.h</span></span>
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<td class="diff-line-num old_line" data-linenumber="49" style="width: 35px; color: rgba(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="49" style="width: 35px; color: rgba(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="LC49" class="line" lang="make"><span class="nl">kmmap.o</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">kmmap.h hashmapkma.h</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="56" style="width: 35px; color: rgba(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="56" style="width: 35px; color: rgba(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">@@ -56,16 +56,17 @@ printconsensus.o: printconsensus.h assembly.h</td>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="make"><span class="nl">qseqs.o</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">qseqs.h pherror.h</span></span>
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57
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57
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="make"><span class="nl">qualcheck.o</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">qualcheck.h compdna.h hashmap.h pherror.h stdnuc.h stdstat.h</span></span>
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58
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58
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="make"><span class="nl">runinput.o</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">runinput.h compdna.h filebuff.h pherror.h qseqs.h seqparse.h</span></span>
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59
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="make"><span class="nl">runkma.o</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">runkma.h align.h alnfrags.h assembly.h chain.h compdna.h ef.h filebuff.h frags.h hashmapindex.h kmapipe.h nw.h pherror.h printconsensus.h qseqs.h stdnuc.h stdstat.h vcf.h</span></span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="make"><span class="nl">runkma.o</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">runkma.h align.h alnfrags.h assembly.h chain.h compdna.h ef.h filebuff.h frags.h hashmapindex.h kmapipe.h nw.h pherror.h printconsensus.h qseqs.h stdnuc.h stdstat.h <span class="idiff left right">tmp.h </span>vcf.h</span></span>
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60
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60
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="make"><span class="nl">sam.o</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">sam.h nw.h pherror.h qseqs.h runkma.h</span></span>
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61
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61
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="make"><span class="nl">savekmers.o</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">savekmers.h ankers.h compdna.h hashmapkma.h penalties.h pherror.h qseqs.h stdnuc.h stdstat.h threader.h</span></span>
</pre>
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62
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62
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="make"><span class="nl">seq2fasta.o</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">seq2fasta.h pherror.h qseqs.h runkma.h stdnuc.h</span></span>
</pre>
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63
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63
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="make"><span class="nl">seqparse.o</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">seqparse.h filebuff.h qseqs.h</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="64" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
64
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<td class="diff-line-num new_line" data-linenumber="64" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
64
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="make"><span class="nl">shm.o</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">shm.h pherror.h hashmapkma.h version.h</span></span>
</pre>
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65
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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="make"><span class="nl">sparse.o</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">sparse.h compkmers.h hashtable.h kmapipe.h pherror.h runinput.h savekmers.h stdnuc.h stdstat.h</span></span>
</pre>
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66
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<pre style="margin: 0;">-<span id="LC66" class="line" lang="make"><span class="nl">spltdb.o</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">spltdb.h align.h alnfrags.h assembly.h chain.h compdna.h ef.h filebuff.h frags.h hashmapindex.h kmapipe.h nw.h pherror.h printconsensus.h qseqs.h runkma.h stdnuc.h stdstat.h vcf.h</span></span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="make"><span class="nl">spltdb.o</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">spltdb.h align.h alnfrags.h assembly.h chain.h compdna.h ef.h filebuff.h frags.h hashmapindex.h kmapipe.h nw.h pherror.h printconsensus.h qseqs.h runkma.h stdnuc.h stdstat.h <span class="idiff left right">tmp.h </span>vcf.h</span></span>
</pre>
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67
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67
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="make"><span class="nl">stdnuc.o</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">stdnuc.h</span></span>
</pre>
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68
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68
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="make"><span class="nl">stdstat.o</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">stdstat.h</span></span>
</pre>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="make"><span class="nl">tmp.o</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">tmp.h pherror.h threader.h</span></span>
</pre>
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69
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<td class="diff-line-num new_line" data-linenumber="70" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
70
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="make"><span class="nl">update.o</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">update.h hashmapkma.h pherror.h stdnuc.h</span></span>
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70
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<td class="diff-line-num new_line" data-linenumber="71" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
71
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="make"><span class="nl">updateindex.o</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">updateindex.h compdna.h hashmap.h hashmapindex.h pherror.h qualcheck.h stdnuc.h pherror.h</span></span>
</pre>
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71
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72
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="make"><span class="nl">updatescores.o</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">updatescores.h qseqs.h</span></span>
</pre>
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<br>
</li>
<li id="ddd34e1789cc70e19fb0e89d73fae8d104ed9c40">
<a href="https://salsa.debian.org/med-team/kma/commit/f5137c3d39949889292033da254f861b4981ebbf#ddd34e1789cc70e19fb0e89d73fae8d104ed9c40"><strong>align.c</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="48" style="width: 35px; color: rgba(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="48" style="width: 35px; color: rgba(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">@@ -48,6 +48,7 @@ AlnScore KMA(const HashMap_index *template_index, const unsigned char *qseq, int</td>
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48
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48
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="c"> <span class="n" style="color: #333;">mask</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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49
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49
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="c"> <span class="n" style="color: #333;">mask</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="o" style="font-weight: 600;">~</span><span class="n" style="color: #333;">mask</span><span class="p">)</span> <span class="o" style="font-weight: 600;">>></span> <span class="p">(</span><span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="p">(</span><span class="n" style="color: #333;">kmersize</span> <span class="o" style="font-weight: 600;"><<</span> <span class="mi" style="color: #099;">1</span><span class="p">));</span></span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="c"> <span class="n" style="color: #333;">key</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="LC51" class="line" lang="c"> </span>
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51
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52
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* circular, skip boundaries */</span></span>
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53
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">min</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">max</span><span class="p">)</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 class="n" style="color: #333;">min</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="757" style="width: 35px; color: rgba(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="758" style="width: 35px; color: rgba(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">@@ -757,6 +758,7 @@ int anker_rc(const HashMap_index *template_index, unsigned char *qseq, int q_len</td>
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757
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758
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<pre style="margin: 0;"> <span id="LC758" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">==</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="p">{</span></span>
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758
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759
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<pre style="margin: 0;"> <span id="LC759" class="line" lang="c"> <span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">q_len</span><span class="p">;</span></span>
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759
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760
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<pre style="margin: 0;"> <span id="LC760" class="line" lang="c"> <span class="p">}</span></span>
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761
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<pre style="margin: 0;">+<span id="LC761" class="line" lang="c"> </span>
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760
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762
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<pre style="margin: 0;"> <span id="LC762" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">kmersize</span><span class="p">)</span> <span class="p">{</span></span>
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761
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763
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<pre style="margin: 0;"> <span id="LC763" class="line" lang="c"> <span class="n" style="color: #333;">key</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">makeKmer</span><span class="p">(</span><span class="n" style="color: #333;">qseq</span><span class="p">,</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">kmersize</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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762
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764
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<pre style="margin: 0;"> <span id="LC764" class="line" lang="c"> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">+=</span> <span class="p">(</span><span class="n" style="color: #333;">kmersize</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 unfold js-unfold new_line" data-linenumber="769" style="width: 35px; color: rgba(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">@@ -767,6 +769,7 @@ int anker_rc(const HashMap_index *template_index, unsigned char *qseq, int q_len</td>
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767
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769
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<pre style="margin: 0;"> <span id="LC769" 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="n" style="color: #333;">end</span><span class="p">)</span> <span class="p">{</span></span>
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768
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770
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<pre style="margin: 0;"> <span id="LC770" class="line" lang="c"> <span class="n" style="color: #333;">key</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">((</span><span class="n" style="color: #333;">key</span> <span class="o" style="font-weight: 600;"><<</span> <span class="mi" style="color: #099;">2</span><span class="p">)</span> <span class="o" style="font-weight: 600;">|</span> <span class="n" style="color: #333;">qseq</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;">mask</span><span class="p">;</span></span>
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769
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771
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<pre style="margin: 0;"> <span id="LC771" class="line" lang="c"> <span class="n" style="color: #333;">value</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">hashMap_index_get_bound</span><span class="p">(</span><span class="n" style="color: #333;">template_index</span><span class="p">,</span> <span class="n" style="color: #333;">key</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;">shifter</span><span class="p">);</span></span>
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772
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<pre style="margin: 0;">+<span id="LC772" class="line" lang="c"> </span>
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770
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773
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<pre style="margin: 0;"> <span id="LC773" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">value</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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771
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774
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<pre style="margin: 0;"> <span id="LC774" class="line" lang="c"> <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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772
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<pre style="margin: 0;"> <span id="LC775" 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="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">value</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -870,6 +873,8 @@ int anker_rc(const HashMap_index *template_index, unsigned char *qseq, int q_len</td>
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873
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<pre style="margin: 0;"> <span id="LC873" class="line" lang="c"> </span>
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874
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<pre style="margin: 0;"> <span id="LC874" class="line" lang="c"> <span class="n" style="color: #333;">stop</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">hashMap_index_getNextDubPos</span><span class="p">(</span><span class="n" style="color: #333;">template_index</span><span class="p">,</span> <span class="n" style="color: #333;">key</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;">stop</span><span class="p">,</span> <span class="n" style="color: #333;">shifter</span><span class="p">);</span></span>
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875
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<pre style="margin: 0;"> <span id="LC875" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC876" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* add best anker score */</span></span>
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<pre style="margin: 0;">+<span id="LC877" class="line" lang="c"> <span class="n" style="color: #333;">score_r</span> <span class="o" style="font-weight: 600;">+=</span> <span class="p">(</span><span class="n" style="color: #333;">bias</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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878
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<pre style="margin: 0;"> <span id="LC878" 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;">bias</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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879
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<pre style="margin: 0;"> <span id="LC879" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC880" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* update position */</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">@@ -883,6 +888,7 @@ int anker_rc(const HashMap_index *template_index, unsigned char *qseq, int q_len</td>
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<pre style="margin: 0;"> <span id="LC888" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC889" 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;">end</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC890" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC891" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC892" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">bestScore</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">score_r</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC893" class="line" lang="c"> <span class="n" style="color: #333;">bestScore</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">score_r</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC894" class="line" lang="c"> <span class="p">}</span></span>
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<li id="150c159b696c4d2657c933fc25c1f6af0b301fe2">
<a href="https://salsa.debian.org/med-team/kma/commit/f5137c3d39949889292033da254f861b4981ebbf#150c159b696c4d2657c933fc25c1f6af0b301fe2"><strong>compress.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">@@ -702,6 +702,7 @@ HashMapKMA * compressKMA_megaDB(HashMap *templates, FILE *out) {</td>
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<pre style="margin: 0;"> <span id="LC702" 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;">"# Overflow bypassed.</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="LC703" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC704" class="line" lang="c"> <span class="n" style="color: #333;">free</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;">values</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC705" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC706" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* convert valuesHash to a linked list */</span></span>
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706
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707
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<pre style="margin: 0;"> <span id="LC707" class="line" lang="c"> <span class="n" style="color: #333;">table</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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707
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708
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<pre style="margin: 0;"> <span id="LC708" 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;">shmValues</span><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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<a href="https://salsa.debian.org/med-team/kma/commit/f5137c3d39949889292033da254f861b4981ebbf#6f01b21e666698a62c6dd6fcadb36a64d4bc30d4"><strong>frags.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">@@ -24,6 +24,7 @@</td>
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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 "pherror.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 "qseqs.h"</span></span>
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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 "threader.h"</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "tmp.h"</span></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="c"></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;">FILE</span> <span class="o" style="font-weight: 600;">*</span> <span class="nf" style="color: #900; font-weight: 600;">printFrags</span><span class="p">(</span><span class="n" style="color: #333;">Frag</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">alignFrags</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">DB_size</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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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -31,7 +32,7 @@ FILE * printFrags(Frag **alignFrags, int DB_size) {</td>
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<pre style="margin: 0;"> <span id="LC32" 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;">OUT</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;">Frag</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">alignFrag</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">next</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="c"> </span>
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<pre style="margin: 0;">-<span id="LC34" 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="p">(</span><span class="n" style="color: #333;">OUT</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tmp<span class="idiff left">file</span></span><span class="p"><span class="idiff right">(</span>)))</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC35" 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="p">(</span><span class="n" style="color: #333;">OUT</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tmp<span class="idiff left">F</span></span><span class="p"><span class="idiff">(</span></span><span class="mi" style="color: #099;"><span class="idiff right">0</span></span><span class="p">)))</span> <span 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;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"Could not create tmp files.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="c"> <span class="n" style="color: #333;">ERROR</span><span class="p">();</span></span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="c"> <span class="p">}</span></span>
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<a href="https://salsa.debian.org/med-team/kma/commit/f5137c3d39949889292033da254f861b4981ebbf#7eed163ea0757dada23cd667898abf840233da45"><strong>index.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">@@ -497,9 +497,13 @@ int index_main(int argc, char *argv[]) {</td>
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<pre style="margin: 0;"> <span id="LC497" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">templatefilename</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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498
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498
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<pre style="margin: 0;"> <span id="LC498" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* load */</span></span>
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<pre style="margin: 0;"> <span id="LC499" 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;">"# Loading database: %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;">outputfilename</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC500" class="line" lang="c"> <span class="n" style="color: #333;">finalDB</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">load_DBs</span><span class="p">(</span><span class="n" style="color: #333;">templatefilename</span><span class="p">,</span> <span class="n" style="color: #333;">outputfilename</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">template_lengths</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">template_ulengths</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">template_slengths</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC500" class="line" lang="c"> <span class="n" style="color: #333;">finalDB</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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<pre style="margin: 0;">+<span id="LC501" class="line" lang="c"> <span class="n" style="color: #333;">kmerindex</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">load_DBs</span><span class="p">(</span><span class="n" style="color: #333;">templatefilename</span><span class="p">,</span> <span class="n" style="color: #333;">outputfilename</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">template_lengths</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">template_ulengths</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">template_slengths</span><span class="p">,</span> <span class="n" style="color: #333;">finalDB</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC502" class="line" lang="c"> <span class="n" style="color: #333;">kmersize</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">finalDB</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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<pre style="margin: 0;">-<span id="LC502" class="line" lang="c"> <span class="n" style="color: #333;">kmerindex</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">template_lengths</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC503" class="line" lang="c"> <span class="n" style="color: #333;">mask</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="LC504" class="line" lang="c"> <span class="n" style="color: #333;">mask</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="o" style="font-weight: 600;">~</span><span class="n" style="color: #333;">mask</span><span class="p">)</span> <span class="o" style="font-weight: 600;">>></span> <span class="p">(</span><span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="p">(</span><span class="n" style="color: #333;">kmersize</span> <span class="o" style="font-weight: 600;"><<</span> <span class="mi" style="color: #099;">1</span><span class="p">));</span></span>
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<pre style="margin: 0;">+<span id="LC505" 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;">finalDB</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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<pre style="margin: 0;">+<span id="LC506" class="line" lang="c"> <span class="n" style="color: #333;">prefix_len</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">finalDB</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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<pre style="margin: 0;"> <span id="LC507" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC508" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* determine params based on loaded DB */</span></span>
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<pre style="margin: 0;"> <span id="LC509" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">prefix_len</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">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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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -598,7 +602,6 @@ int index_main(int argc, char *argv[]) {</td>
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<pre style="margin: 0;"> <span id="LC602" class="line" lang="c"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">template_lengths</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1024</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC603" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC604" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC601" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC605" 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;">"# Indexing databases.</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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606
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<pre style="margin: 0;"> <span id="LC606" class="line" lang="c"> <span class="n" style="color: #333;">t0</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">clock</span><span class="p">();</span></span>
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604
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607
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<pre style="margin: 0;"> <span id="LC607" class="line" lang="c"> <span class="n" style="color: #333;">makeDB</span><span class="p">(</span><span class="n" style="color: #333;">templates</span><span class="p">,</span> <span class="n" style="color: #333;">kmerindex</span><span class="p">,</span> <span class="n" style="color: #333;">inputfiles</span><span class="p">,</span> <span class="n" style="color: #333;">filecount</span><span class="p">,</span> <span class="n" style="color: #333;">outputfilename</span><span class="p">,</span> <span class="n" style="color: #333;">appender</span><span class="p">,</span> <span class="n" style="color: #333;">to2Bit</span><span class="p">,</span> <span class="n" style="color: #333;">MinLen</span><span class="p">,</span> <span class="n" style="color: #333;">MinKlen</span><span class="p">,</span> <span class="n" style="color: #333;">homQ</span><span class="p">,</span> <span class="n" style="color: #333;">homT</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">template_lengths</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">template_ulengths</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">template_slengths</span><span class="p">);</span></span>
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<a href="https://salsa.debian.org/med-team/kma/commit/f5137c3d39949889292033da254f861b4981ebbf#5bb411548ec4b39482e6de83d3ad98f29b1162b1"><strong>kma.c</strong></a>
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<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -41,6 +41,7 @@</td>
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41
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41
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "sparse.h"</span></span>
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42
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42
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "spltdb.h"</span></span>
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43
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43
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "stdstat.h"</span></span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "tmp.h"</span></span>
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44
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45
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "vcf.h"</span></span>
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45
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46
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "version.h"</span></span>
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46
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47
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="c"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="137" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="138" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -137,6 +138,7 @@ static void helpMessage(int exeStatus) {</td>
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137
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138
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<pre style="margin: 0;"> <span id="LC138" 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;">-apm</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">Sets both pm and fpm</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">u</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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138
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<td class="diff-line-num new_line" data-linenumber="139" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
139
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<pre style="margin: 0;"> <span id="LC139" class="line" lang="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;">-shm</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">Use shared DB made by kma_shm</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">0 (lvl)</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="139" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
139
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<td class="diff-line-num new_line" data-linenumber="140" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
140
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<pre style="margin: 0;"> <span id="LC140" class="line" lang="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;">-mmap</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">Memory map *.comp.by</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="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;">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;">-tmp</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">Set directory for temporary files.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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140
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<td class="diff-line-num new_line" data-linenumber="142" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
142
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<pre style="margin: 0;"> <span id="LC142" class="line" lang="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;">-1t1</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">Force end to end mapping</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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141
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<td class="diff-line-num new_line" data-linenumber="143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
143
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<pre style="margin: 0;"> <span id="LC143" 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;">-ck</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">Count kmers instead of</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">#</span><span class="se" style="color: #d14;">\t\t\t</span><span class="s" style="color: #d14;">pseudo alignment</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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142
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<td class="diff-line-num new_line" data-linenumber="144" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
144
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<pre style="margin: 0;"> <span id="LC144" 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;">-ca</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">Make circular alignments</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 unfold js-unfold old_line" data-linenumber="167" style="width: 35px; color: rgba(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="169" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -167,13 +169,13 @@ int kma_main(int argc, char *argv[]) {</td>
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<td class="diff-line-num old_line" data-linenumber="167" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
167
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169
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<pre style="margin: 0;"> <span id="LC169" class="line" lang="c"> <span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">minPhred</span><span class="p">,</span> <span class="n" style="color: #333;">fiveClip</span><span class="p">,</span> <span class="n" style="color: #333;">sparse_run</span><span class="p">,</span> <span class="n" style="color: #333;">mem_mode</span><span class="p">,</span> <span class="n" style="color: #333;">Mt1</span><span class="p">,</span> <span class="n" style="color: #333;">ConClave</span><span class="p">,</span> <span class="n" style="color: #333;">bcd</span><span class="p">;</span></span>
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168
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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;">static</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">fileCounter</span><span class="p">,</span> <span class="n" style="color: #333;">fileCounter_PE</span><span class="p">,</span> <span class="n" style="color: #333;">fileCounter_INT</span><span class="p">,</span> <span class="n" style="color: #333;">targetNum</span><span class="p">,</span> <span class="n" style="color: #333;">vcf</span><span class="p">;</span></span>
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169
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171
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<pre style="margin: 0;"> <span id="LC171" class="line" lang="c"> <span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">extendedFeatures</span><span class="p">,</span> <span class="n" style="color: #333;">spltDB</span><span class="p">,</span> <span class="n" style="color: #333;">mq</span><span class="p">,</span> <span class="n" style="color: #333;">thread_num</span><span class="p">,</span> <span class="n" style="color: #333;">kmersize</span><span class="p">,</span> <span class="n" style="color: #333;">one2one</span><span class="p">;</span></span>
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170
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<td class="diff-line-num new_line old" data-linenumber="172" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC170" class="line" lang="c"> <span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ref_fsa</span><span class="p">,</span> <span class="n" style="color: #333;">print_matrix</span><span class="p">,</span> <span class="n" style="color: #333;">print_all</span><span class="p">,</span> <span class="n" style="color: #333;">sam</span><span class="p">,</span> <span class="o" style="font-weight: 600;"><span class="idiff left">**</span></span><span class="n" style="color: #333;"><span class="idiff">d</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">W1</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">U</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">M</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">MM</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">PE</span></span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="172" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="c"> <span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ref_fsa</span><span class="p">,</span> <span class="n" style="color: #333;">print_matrix</span><span class="p">,</span> <span class="n" style="color: #333;">print_all</span><span class="p">,</span> <span class="n" style="color: #333;">sam</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">Ts</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">Tv</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">**</span></span><span class="n" style="color: #333;"><span class="idiff right">d</span></span><span class="p">;</span></span>
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171
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173
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<pre style="margin: 0;"> <span id="LC173" class="line" lang="c"> <span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">nc</span><span class="p">,</span> <span class="n" style="color: #333;">nf</span><span class="p">,</span> <span class="n" style="color: #333;">shm</span><span class="p">,</span> <span class="n" style="color: #333;">exhaustive</span><span class="p">;</span></span>
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172
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<td class="diff-line-num new_line" data-linenumber="174" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
174
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<pre style="margin: 0;"> <span id="LC174" class="line" lang="c"> <span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">outputfilename</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">templatefilename</span><span class="p">,</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">templatefilenames</span><span class="p">;</span></span>
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173
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<td class="diff-line-num new_line" data-linenumber="175" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
175
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<pre style="margin: 0;"> <span id="LC175" class="line" lang="c"> <span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">inputfiles</span><span class="p">,</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">inputfiles_PE</span><span class="p">,</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">inputfiles_INT</span><span class="p">,</span> <span class="n" style="color: #333;">ss</span><span class="p">;</span></span>
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174
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<td class="diff-line-num new_line" data-linenumber="176" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
176
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<pre style="margin: 0;"> <span id="LC176" class="line" lang="c"> <span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">ID_t</span><span class="p">,</span> <span class="n" style="color: #333;">scoreT</span><span class="p">,</span> <span class="n" style="color: #333;">evalue</span><span class="p">;</span></span>
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175
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<td class="diff-line-num new_line" data-linenumber="177" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
177
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<pre style="margin: 0;"> <span id="LC177" class="line" lang="c"> <span class="k" style="font-weight: 600;">static</span> <span class="n" style="color: #333;">Penalties</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">rewards</span><span class="p">;</span></span>
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176
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<pre style="margin: 0;">-<span id="LC176" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">j</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">,</span> <span class="n" style="color: #333;">exe_len</span><span class="p">,</span> <span class="n" style="color: #333;">status</span><span class="p">,</span> <span class="n" style="color: #333;">size</span><span class="p">,</span> <span class="n" style="color: #333;">escape</span><span class="p">,</span> <span class="n" style="color: #333;">step1</span><span class="p">,</span> <span class="n" style="color: #333;">step2</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="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">j</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">,</span> <span class="n" style="color: #333;">exe_len</span><span class="p">,</span> <span class="n" style="color: #333;">status</span><span class="p">,</span> <span class="n" style="color: #333;">size</span><span class="p">,</span> <span class="n" style="color: #333;">escape</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">tmp</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">step1</span><span class="p">,</span> <span class="n" style="color: #333;">step2</span><span class="p">;</span></span>
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177
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179
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<pre style="margin: 0;"> <span id="LC179" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">totFrags</span><span class="p">;</span></span>
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178
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180
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<pre style="margin: 0;"> <span id="LC180" 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;">to2Bit</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="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">myTemplatefilename</span><span class="p">;</span></span>
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179
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181
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<pre style="margin: 0;"> <span id="LC181" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">support</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="223" style="width: 35px; color: rgba(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="225" style="width: 35px; color: rgba(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">@@ -223,16 +225,22 @@ int kma_main(int argc, char *argv[]) {</td>
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223
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225
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<pre style="margin: 0;"> <span id="LC225" class="line" lang="c"> <span class="n" style="color: #333;">one2one</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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224
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226
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<pre style="margin: 0;"> <span id="LC226" class="line" lang="c"> <span class="n" style="color: #333;">ss</span> <span class="o" style="font-weight: 600;">=</span> <span class="sc" style="color: #d14;">'q'</span><span class="p">;</span></span>
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225
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227
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<pre style="margin: 0;"> <span id="LC227" class="line" lang="c"> <span class="n" style="color: #333;">mem_mode</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="LC226" class="line" lang="c"> <span class="n" style="color: #333;">M</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC227" class="line" lang="c"> <span class="n" style="color: #333;">MM</span> <span class="o" style="font-weight: 600;">=</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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228
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<pre style="margin: 0;">-<span id="LC228" class="line" lang="c"> <span class="n" style="color: #333;">W1</span> <span class="o" style="font-weight: 600;">=</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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229
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<pre style="margin: 0;">-<span id="LC229" class="line" lang="c"> <span class="n" style="color: #333;">U</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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230
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<pre style="margin: 0;">-<span id="LC230" class="line" lang="c"> <span class="n" style="color: #333;">PE</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">7</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="c"> <span class="n" style="color: #333;">rewards</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;">Penalties</span><span class="p">));</span></span>
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229
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="c"> <span class="n" style="color: #333;">rewards</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">M</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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230
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<pre style="margin: 0;">+<span id="LC230" class="line" lang="c"> <span class="n" style="color: #333;">rewards</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">MM</span> <span class="o" style="font-weight: 600;">=</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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231
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<pre style="margin: 0;">+<span id="LC231" class="line" lang="c"> <span class="n" style="color: #333;">rewards</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">U</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC232" class="line" lang="c"> <span class="n" style="color: #333;">rewards</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">W1</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">3</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC233" class="line" lang="c"> <span class="n" style="color: #333;">rewards</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Wl</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">6</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC234" class="line" lang="c"> <span class="n" style="color: #333;">rewards</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Mn</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="c"> <span class="n" style="color: #333;">rewards</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">PE</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">7</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC236" class="line" lang="c"> <span class="n" style="color: #333;">Tv</span> <span class="o" style="font-weight: 600;">=</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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237
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="c"> <span class="n" style="color: #333;">Ts</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">2</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC238" class="line" lang="c"> <span class="n" style="color: #333;">thread_num</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC239" class="line" lang="c"> <span class="n" style="color: #333;">inputfiles_PE</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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233
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<pre style="margin: 0;"> <span id="LC240" class="line" lang="c"> <span class="n" style="color: #333;">inputfiles_INT</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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241
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<pre style="margin: 0;"> <span id="LC241" class="line" lang="c"> <span class="n" style="color: #333;">inputfiles</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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235
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<pre style="margin: 0;"> <span id="LC242" class="line" lang="c"> <span class="n" style="color: #333;">templatefilenames</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="LC243" class="line" lang="c"> <span class="n" style="color: #333;">tmp</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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236
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244
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<pre style="margin: 0;"> <span id="LC244" class="line" lang="c"> <span class="n" style="color: #333;">Mt1</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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237
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245
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<pre style="margin: 0;"> <span id="LC245" class="line" lang="c"> <span class="n" style="color: #333;">inputfiles</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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238
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246
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<pre style="margin: 0;"> <span id="LC246" class="line" lang="c"> <span class="n" style="color: #333;">deConPrintPtr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">printPtr</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="618" style="width: 35px; color: rgba(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="626" style="width: 35px; color: rgba(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">@@ -618,8 +626,8 @@ int kma_main(int argc, char *argv[]) {</td>
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618
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626
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<pre style="margin: 0;"> <span id="LC626" 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;">"-reward"</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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619
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627
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<pre style="margin: 0;"> <span id="LC627" 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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620
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628
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<pre style="margin: 0;"> <span id="LC628" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">args</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">argc</span><span class="p">)</span> <span class="p">{</span></span>
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621
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<pre style="margin: 0;">-<span id="LC621" class="line" lang="c"> <span class="n" style="color: #333;">M</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">strtol</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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622
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<pre style="margin: 0;">-<span id="LC622" class="line" lang="c"> <span class="n" style="color: #333;"><span class="idiff left">M</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">abs</span></span><span class="p"><span class="idiff right">(</span></span><span class="n" style="color: #333;">M</span><span class="p">);</span></span>
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<td class="diff-line-num new old_line" data-linenumber="623" style="width: 35px; color: rgba(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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629
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<pre style="margin: 0;">+<span id="LC629" class="line" lang="c"> <span class="n" style="color: #333;"><span class="idiff left">rewards</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">-></span></span><span class="n" style="color: #333;">M</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">strtol</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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630
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<pre style="margin: 0;">+<span id="LC630" class="line" lang="c"> <span class="n" style="color: #333;"><span class="idiff left">rewards</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">M</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">abs</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">rewards</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">-></span></span><span class="n" style="color: #333;">M</span><span class="p">);</span></span>
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623
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631
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<pre style="margin: 0;"> <span id="LC631" 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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624
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632
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<pre style="margin: 0;"> <span id="LC632" 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;">-reward</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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625
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633
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<pre style="margin: 0;"> <span id="LC633" 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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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="628" style="width: 35px; color: rgba(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="636" style="width: 35px; color: rgba(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">@@ -628,8 +636,8 @@ int kma_main(int argc, char *argv[]) {</td>
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628
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<pre style="margin: 0;"> <span id="LC636" 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;">"-penalty"</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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629
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637
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<pre style="margin: 0;"> <span id="LC637" 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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638
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<pre style="margin: 0;"> <span id="LC638" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">args</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">argc</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC631" class="line" lang="c"> <span class="n" style="color: #333;">MM</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">strtol</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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<pre style="margin: 0;">-<span id="LC632" class="line" lang="c"> <span class="n" style="color: #333;"><span class="idiff left">MM</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">MIN</span></span><span class="p"><span class="idiff">(</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="n" style="color: #333;"><span class="idiff">MM</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">MM</span><span class="p">);</span></span>
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639
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<pre style="margin: 0;">+<span id="LC639" class="line" lang="c"> <span class="n" style="color: #333;"><span class="idiff left">rewards</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">-></span></span><span class="n" style="color: #333;">MM</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">strtol</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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640
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<pre style="margin: 0;">+<span id="LC640" class="line" lang="c"> <span class="n" style="color: #333;"><span class="idiff left">rewards</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">MM</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">MIN</span></span><span class="p"><span class="idiff">(</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="n" style="color: #333;"><span class="idiff">rewards</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">MM</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">rewards</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">-></span></span><span class="n" style="color: #333;">MM</span><span class="p">);</span></span>
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641
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<pre style="margin: 0;"> <span id="LC641" 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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634
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642
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<pre style="margin: 0;"> <span id="LC642" 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;">-penalty</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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643
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<pre style="margin: 0;"> <span id="LC643" 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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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="638" style="width: 35px; color: rgba(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="646" style="width: 35px; color: rgba(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">@@ -638,8 +646,8 @@ int kma_main(int argc, char *argv[]) {</td>
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638
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646
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<pre style="margin: 0;"> <span id="LC646" 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;">"-gapopen"</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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647
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<pre style="margin: 0;"> <span id="LC647" 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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648
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<pre style="margin: 0;"> <span id="LC648" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">args</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">argc</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC641" class="line" lang="c"> <span class="n" style="color: #333;">W1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">strtol</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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642
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<pre style="margin: 0;">-<span id="LC642" class="line" lang="c"> <span class="n" style="color: #333;"><span class="idiff left">W1</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">MIN</span></span><span class="p"><span class="idiff">(</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="n" style="color: #333;"><span class="idiff">W1</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">W1</span><span class="p">);</span></span>
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649
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<pre style="margin: 0;">+<span id="LC649" class="line" lang="c"> <span class="n" style="color: #333;"><span class="idiff left">rewards</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">-></span></span><span class="n" style="color: #333;">W1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">strtol</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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650
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<pre style="margin: 0;">+<span id="LC650" class="line" lang="c"> <span class="n" style="color: #333;"><span class="idiff left">rewards</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">W1</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">MIN</span></span><span class="p"><span class="idiff">(</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="n" style="color: #333;"><span class="idiff">rewards</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">W1</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">rewards</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">-></span></span><span class="n" style="color: #333;">W1</span><span class="p">);</span></span>
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651
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<pre style="margin: 0;"> <span id="LC651" 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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652
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<pre style="margin: 0;"> <span id="LC652" 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;">-gapopen</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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653
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<pre style="margin: 0;"> <span id="LC653" 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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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="648" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -648,23 +656,71 @@ int kma_main(int argc, char *argv[]) {</td>
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648
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656
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<pre style="margin: 0;"> <span id="LC656" 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;">"-gapextend"</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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649
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657
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<pre style="margin: 0;"> <span id="LC657" 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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650
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658
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<pre style="margin: 0;"> <span id="LC658" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">args</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">argc</span><span class="p">)</span> <span class="p">{</span></span>
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651
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<pre style="margin: 0;">-<span id="LC651" class="line" lang="c"> <span class="n" style="color: #333;">U</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">strtol</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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652
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<pre style="margin: 0;">-<span id="LC652" class="line" lang="c"> <span class="n" style="color: #333;"><span class="idiff left">U</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">MIN</span></span><span class="p"><span class="idiff">(</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="n" style="color: #333;"><span class="idiff">U</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">U</span><span class="p">);</span></span>
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659
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<pre style="margin: 0;">+<span id="LC659" class="line" lang="c"> <span class="n" style="color: #333;"><span class="idiff left">rewards</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">-></span></span><span class="n" style="color: #333;">U</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">strtol</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="660" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
660
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<pre style="margin: 0;">+<span id="LC660" class="line" lang="c"> <span class="n" style="color: #333;"><span class="idiff left">rewards</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">U</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">MIN</span></span><span class="p"><span class="idiff">(</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="n" style="color: #333;"><span class="idiff">rewards</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">U</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">rewards</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">-></span></span><span class="n" style="color: #333;">U</span><span class="p">);</span></span>
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653
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661
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<pre style="margin: 0;"> <span id="LC661" 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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654
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662
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<pre style="margin: 0;"> <span id="LC662" 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;">-gapextend</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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655
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663
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<pre style="margin: 0;"> <span id="LC663" 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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656
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664
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<pre style="margin: 0;"> <span id="LC664" class="line" lang="c"> <span class="p">}</span></span>
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657
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665
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<pre style="margin: 0;"> <span id="LC665" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC666" 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;">"-localopen"</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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667
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<pre style="margin: 0;">+<span id="LC667" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* here */</span></span>
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668
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<pre style="margin: 0;">+<span id="LC668" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* add to help */</span></span>
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669
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<pre style="margin: 0;">+<span id="LC669" 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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670
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<pre style="margin: 0;">+<span id="LC670" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">args</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">argc</span><span class="p">)</span> <span class="p">{</span></span>
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671
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<pre style="margin: 0;">+<span id="LC671" class="line" lang="c"> <span class="n" style="color: #333;">rewards</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Wl</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">strtol</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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672
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<pre style="margin: 0;">+<span id="LC672" class="line" lang="c"> <span class="n" style="color: #333;">rewards</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Wl</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">MIN</span><span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">rewards</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Wl</span><span class="p">,</span> <span class="n" style="color: #333;">rewards</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Wl</span><span class="p">);</span></span>
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673
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<pre style="margin: 0;">+<span id="LC673" 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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674
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<pre style="margin: 0;">+<span id="LC674" 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;">-localopen</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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675
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<pre style="margin: 0;">+<span id="LC675" 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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676
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<pre style="margin: 0;">+<span id="LC676" class="line" lang="c"> <span class="p">}</span></span>
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677
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<pre style="margin: 0;">+<span id="LC677" class="line" lang="c"> <span class="p">}</span></span>
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678
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<pre style="margin: 0;">+<span id="LC678" 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;">"-Npenalty"</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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679
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<pre style="margin: 0;">+<span id="LC679" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* here */</span></span>
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680
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<pre style="margin: 0;">+<span id="LC680" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* add to help */</span></span>
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681
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<pre style="margin: 0;">+<span id="LC681" 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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682
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<pre style="margin: 0;">+<span id="LC682" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">args</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">argc</span><span class="p">)</span> <span class="p">{</span></span>
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683
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<pre style="margin: 0;">+<span id="LC683" class="line" lang="c"> <span class="n" style="color: #333;">rewards</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Mn</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">strtol</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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684
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<pre style="margin: 0;">+<span id="LC684" class="line" lang="c"> <span class="n" style="color: #333;">rewards</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Mn</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">MIN</span><span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">rewards</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Mn</span><span class="p">,</span> <span class="n" style="color: #333;">rewards</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Mn</span><span class="p">);</span></span>
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685
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<pre style="margin: 0;">+<span id="LC685" 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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686
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<pre style="margin: 0;">+<span id="LC686" 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;">-localopen</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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687
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<pre style="margin: 0;">+<span id="LC687" 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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<pre style="margin: 0;">+<span id="LC688" class="line" lang="c"> <span class="p">}</span></span>
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689
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<pre style="margin: 0;">+<span id="LC689" class="line" lang="c"> <span class="p">}</span></span>
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658
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690
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<pre style="margin: 0;"> <span id="LC690" 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;">"-per"</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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659
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691
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<pre style="margin: 0;"> <span id="LC691" 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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660
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692
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<pre style="margin: 0;"> <span id="LC692" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">args</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">argc</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC661" class="line" lang="c"> <span class="n" style="color: #333;">PE</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">strtol</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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662
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<pre style="margin: 0;">-<span id="LC662" class="line" lang="c"> <span class="n" style="color: #333;"><span class="idiff left">PE</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">abs</span></span><span class="p"><span class="idiff right">(</span></span><span class="n" style="color: #333;">PE</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="693" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
693
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<pre style="margin: 0;">+<span id="LC693" class="line" lang="c"> <span class="n" style="color: #333;"><span class="idiff left">rewards</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">-></span></span><span class="n" style="color: #333;">PE</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">strtol</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="694" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
694
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<pre style="margin: 0;">+<span id="LC694" class="line" lang="c"> <span class="n" style="color: #333;"><span class="idiff left">rewards</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">PE</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">abs</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">rewards</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">-></span></span><span class="n" style="color: #333;">PE</span><span class="p">);</span></span>
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663
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695
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<pre style="margin: 0;"> <span id="LC695" 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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664
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696
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<pre style="margin: 0;"> <span id="LC696" 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;">-per</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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665
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697
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<pre style="margin: 0;"> <span id="LC697" 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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666
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698
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<pre style="margin: 0;"> <span id="LC698" class="line" lang="c"> <span class="p">}</span></span>
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667
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699
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<pre style="margin: 0;"> <span id="LC699" class="line" lang="c"> <span class="p">}</span></span>
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700
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<pre style="margin: 0;">+<span id="LC700" 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;">"-transition"</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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701
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<pre style="margin: 0;">+<span id="LC701" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* here */</span></span>
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702
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<pre style="margin: 0;">+<span id="LC702" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* add to help */</span></span>
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703
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<pre style="margin: 0;">+<span id="LC703" 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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704
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<pre style="margin: 0;">+<span id="LC704" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">args</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">argc</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="705" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
705
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<pre style="margin: 0;">+<span id="LC705" class="line" lang="c"> <span class="n" style="color: #333;">Ts</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">strtol</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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706
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<pre style="margin: 0;">+<span id="LC706" class="line" lang="c"> <span class="n" style="color: #333;">Ts</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">MIN</span><span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">Ts</span><span class="p">,</span> <span class="n" style="color: #333;">Ts</span><span class="p">);</span></span>
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707
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<pre style="margin: 0;">+<span id="LC707" 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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708
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<pre style="margin: 0;">+<span id="LC708" 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;">-localopen</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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709
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<pre style="margin: 0;">+<span id="LC709" 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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710
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<pre style="margin: 0;">+<span id="LC710" class="line" lang="c"> <span class="p">}</span></span>
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711
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<pre style="margin: 0;">+<span id="LC711" class="line" lang="c"> <span class="p">}</span></span>
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712
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<pre style="margin: 0;">+<span id="LC712" 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;">"-transversion"</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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713
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<pre style="margin: 0;">+<span id="LC713" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* here */</span></span>
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714
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<pre style="margin: 0;">+<span id="LC714" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* add to help */</span></span>
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715
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<pre style="margin: 0;">+<span id="LC715" 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="716" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
716
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<pre style="margin: 0;">+<span id="LC716" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">args</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">argc</span><span class="p">)</span> <span class="p">{</span></span>
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717
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<pre style="margin: 0;">+<span id="LC717" class="line" lang="c"> <span class="n" style="color: #333;">Tv</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">strtol</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="718" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
718
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<pre style="margin: 0;">+<span id="LC718" class="line" lang="c"> <span class="n" style="color: #333;">Tv</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">MIN</span><span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">Tv</span><span class="p">,</span> <span class="n" style="color: #333;">Tv</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="719" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
719
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<pre style="margin: 0;">+<span id="LC719" 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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720
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<pre style="margin: 0;">+<span id="LC720" 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;">-localopen</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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721
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<pre style="margin: 0;">+<span id="LC721" 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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722
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<pre style="margin: 0;">+<span id="LC722" class="line" lang="c"> <span class="p">}</span></span>
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723
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<pre style="margin: 0;">+<span id="LC723" class="line" lang="c"> <span class="p">}</span></span>
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668
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724
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<pre style="margin: 0;"> <span id="LC724" 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;">"-and"</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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669
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725
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<pre style="margin: 0;"> <span id="LC725" class="line" lang="c"> <span class="n" style="color: #333;">cmp</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">cmp_and</span><span class="p">;</span></span>
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670
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726
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<pre style="margin: 0;"> <span id="LC726" 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;">"-boot"</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="727" style="width: 35px; color: rgba(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="783" style="width: 35px; color: rgba(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">@@ -727,11 +783,21 @@ int kma_main(int argc, char *argv[]) {</td>
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727
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783
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<pre style="margin: 0;"> <span id="LC783" 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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728
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<td class="diff-line-num new_line" data-linenumber="784" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
784
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<pre style="margin: 0;"> <span id="LC784" 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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729
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785
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<pre style="margin: 0;"> <span id="LC785" class="line" lang="c"> <span class="n" style="color: #333;">scoreT</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mi" style="color: #099;">75</span><span class="p">;</span></span>
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730
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<pre style="margin: 0;">-<span id="LC730" class="line" lang="c"> <span class="n" style="color: #333;">M</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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731
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<td class="diff-line-num new_line old" data-linenumber="786" style="width: 35px; color: rgba(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="LC731" class="line" lang="c"> <span class="n" style="color: #333;">MM</span> <span class="o" style="font-weight: 600;">=</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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732
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<pre style="margin: 0;">-<span id="LC732" class="line" lang="c"> <span class="n" style="color: #333;">W1</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">5</span><span class="p">;</span></span>
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733
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<td class="diff-line-num new_line old" data-linenumber="786" style="width: 35px; color: rgba(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="LC733" class="line" lang="c"> <span class="n" style="color: #333;">U</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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734
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<td class="diff-line-num new_line old" data-linenumber="786" style="width: 35px; color: rgba(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="LC734" class="line" lang="c"> <span class="n" style="color: #333;">PE</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">17</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="786" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
786
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<pre style="margin: 0;">+<span id="LC786" class="line" lang="c"> <span class="n" style="color: #333;">rewards</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">M</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="787" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
787
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<pre style="margin: 0;">+<span id="LC787" class="line" lang="c"> <span class="n" style="color: #333;">rewards</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">MM</span> <span class="o" style="font-weight: 600;">=</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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788
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<pre style="margin: 0;">+<span id="LC788" class="line" lang="c"> <span class="n" style="color: #333;">rewards</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">W1</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">5</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="789" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
789
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<pre style="margin: 0;">+<span id="LC789" class="line" lang="c"> <span class="n" style="color: #333;">rewards</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">U</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="790" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
790
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<pre style="margin: 0;">+<span id="LC790" class="line" lang="c"> <span class="n" style="color: #333;">rewards</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">PE</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">17</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="791" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
791
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<pre style="margin: 0;">+<span id="LC791" 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;">"-tmp"</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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792
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<pre style="margin: 0;">+<span id="LC792" class="line" lang="c"> <span class="n" style="color: #333;">tmp</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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793
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<pre style="margin: 0;">+<span id="LC793" 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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794
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<pre style="margin: 0;">+<span id="LC794" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</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="mi" style="color: #099;">0</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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795
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<pre style="margin: 0;">+<span id="LC795" class="line" lang="c"> <span class="n" style="color: #333;">tmpF</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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796
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<pre style="margin: 0;">+<span id="LC796" class="line" lang="c"> <span class="n" style="color: #333;">tmp</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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797
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<pre style="margin: 0;">+<span id="LC797" 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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798
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<pre style="margin: 0;">+<span id="LC798" 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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799
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<pre style="margin: 0;">+<span id="LC799" class="line" lang="c"> <span class="p">}</span></span>
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800
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<pre style="margin: 0;">+<span id="LC800" class="line" lang="c"> <span class="p">}</span></span>
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735
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801
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<pre style="margin: 0;"> <span id="LC801" 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;">"-spltDB"</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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736
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802
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<pre style="margin: 0;"> <span id="LC802" class="line" lang="c"> <span class="n" style="color: #333;">spltDB</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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737
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803
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<pre style="margin: 0;"> <span id="LC803" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">strcmp</span><span class="p">(</span><span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="n" style="color: #333;">args</span><span class="p">],</span> <span class="s" style="color: #d14;">"-status"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="782" style="width: 35px; color: rgba(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="848" style="width: 35px; color: rgba(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">@@ -782,40 +848,40 @@ int kma_main(int argc, char *argv[]) {</td>
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782
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848
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<pre style="margin: 0;"> <span id="LC848" 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;">" Too few 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 old_line" data-linenumber="783" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
783
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<td class="diff-line-num new_line" data-linenumber="849" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
849
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<pre style="margin: 0;"> <span id="LC849" 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 old_line" data-linenumber="784" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
784
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<td class="diff-line-num new_line" data-linenumber="850" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
850
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<pre style="margin: 0;"> <span id="LC850" 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 old_line" data-linenumber="785" style="width: 35px; color: rgba(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="851" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
851
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<pre style="margin: 0;">+<span id="LC851" 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;">tmp</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new old_line" data-linenumber="785" style="width: 35px; color: rgba(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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852
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<pre style="margin: 0;">+<span id="LC852" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* set tmp files */</span></span>
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<td class="diff-line-num new new_line" data-linenumber="853" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
853
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<pre style="margin: 0;">+<span id="LC853" class="line" lang="c"> <span class="n" style="color: #333;">tmpF</span><span class="p">(</span><span class="n" style="color: #333;">outputfilename</span><span class="p">);</span></span>
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785
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854
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<pre style="margin: 0;"> <span id="LC854" class="line" lang="c"> <span class="p">}</span></span>
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786
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855
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<pre style="margin: 0;"> <span id="LC855" class="line" lang="c"> </span>
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<td class="diff-line-num old_line" data-linenumber="787" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
787
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<td class="diff-line-num new_line" data-linenumber="856" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
856
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<pre style="margin: 0;"> <span id="LC856" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">fileCounter</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">fileCounter_PE</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">fileCounter_INT</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="788" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
788
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<td class="diff-line-num new_line old" data-linenumber="857" style="width: 35px; color: rgba(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="LC788" class="line" lang="c"> <span class="n" style="color: #333;">inputfiles</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">malloc</span><span class="p">(</span><span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span><span class="p">));</span></span>
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<td class="diff-line-num old old_line" data-linenumber="789" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
789
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<td class="diff-line-num new_line old" data-linenumber="857" style="width: 35px; color: rgba(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="LC789" 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;">inputfiles</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="790" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
790
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<td class="diff-line-num new_line old" data-linenumber="857" style="width: 35px; color: rgba(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="LC790" class="line" lang="c"> <span class="n" style="color: #333;">ERROR</span><span class="p">();</span></span>
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<td class="diff-line-num old old_line" data-linenumber="791" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
791
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<td class="diff-line-num new_line old" data-linenumber="857" style="width: 35px; color: rgba(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="LC791" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num new old_line" data-linenumber="792" style="width: 35px; color: rgba(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="857" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
857
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<pre style="margin: 0;">+<span id="LC857" class="line" lang="c"> <span class="n" style="color: #333;">inputfiles</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="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span><span class="p">));</span></span>
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<td class="diff-line-num old_line" data-linenumber="792" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
792
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<td class="diff-line-num new_line" data-linenumber="858" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
858
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<pre style="margin: 0;"> <span id="LC858" class="line" lang="c"> <span class="n" style="color: #333;">inputfiles</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"--"</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="793" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
793
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<td class="diff-line-num new_line" data-linenumber="859" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
859
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<pre style="margin: 0;"> <span id="LC859" class="line" lang="c"> <span class="n" style="color: #333;">fileCounter</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="794" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
794
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<td class="diff-line-num new_line" data-linenumber="860" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
860
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<pre style="margin: 0;"> <span id="LC860" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="795" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
795
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<td class="diff-line-num new_line" data-linenumber="861" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
861
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<pre style="margin: 0;"> <span id="LC861" class="line" lang="c"> <span class="n" style="color: #333;">status</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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796
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<td class="diff-line-num new_line" data-linenumber="862" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
862
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<pre style="margin: 0;"> <span id="LC862" class="line" lang="c"> </span>
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797
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863
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<pre style="margin: 0;"> <span id="LC863" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* set scoring matrix */</span></span>
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798
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<pre style="margin: 0;">-<span id="LC798" class="line" lang="c"> <span class="n" style="color: #333;">d</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">smalloc</span><span class="p">(</span><span class="mi" style="color: #099;">5</span> <span class="o" style="font-weight: 600;">*</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="p">));</span></span>
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799
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<pre style="margin: 0;">-<span id="LC799" 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="mi" style="color: #099;">4</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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800
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<pre style="margin: 0;">-<span id="LC800" class="line" lang="c"> <span class="n" style="color: #333;">d</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;">smalloc</span><span class="p">(</span><span class="mi" style="color: #099;">5</span> <span class="o" style="font-weight: 600;">*</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">));</span></span>
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801
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<pre style="margin: 0;">-<span id="LC801" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">4</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">j</span><span class="p">)</span> <span class="p">{</span></span>
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802
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<pre style="margin: 0;">-<span id="LC802" class="line" lang="c"> <span class="n" style="color: #333;">d</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">][</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">MM</span><span class="p">;</span></span>
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864
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<pre style="margin: 0;">+<span id="LC864" class="line" lang="c"> <span class="n" style="color: #333;">rewards</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">MM</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">Ts</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">Tv</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="mi" style="color: #099;">2</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/* avg. of transition and transversion, rounded down */</span></span>
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865
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<pre style="margin: 0;">+<span id="LC865" class="line" lang="c"> <span class="n" style="color: #333;">d</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">smalloc</span><span class="p">(</span><span class="mi" style="color: #099;">5</span> <span class="o" style="font-weight: 600;">*</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">25</span> <span class="o" style="font-weight: 600;">*</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">));</span></span>
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866
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<pre style="margin: 0;">+<span id="LC866" class="line" lang="c"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">d</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="p">)</span> <span class="p">(</span><span class="n" style="color: #333;">d</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">5</span><span class="p">);</span></span>
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867
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<pre style="margin: 0;">+<span id="LC867" class="line" lang="c"> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="868" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
868
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<pre style="margin: 0;">+<span id="LC868" 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="mi" style="color: #099;">4</span><span class="p">)</span> <span class="p">{</span></span>
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869
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<pre style="margin: 0;">+<span id="LC869" class="line" lang="c"> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">4</span><span class="p">;</span></span>
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870
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<pre style="margin: 0;">+<span id="LC870" class="line" lang="c"> <span class="n" style="color: #333;">d</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">][</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rewards</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Mn</span><span class="p">;</span></span>
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871
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<pre style="margin: 0;">+<span id="LC871" class="line" lang="c"> <span class="k" style="font-weight: 600;">while</span><span class="p">(</span><span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">--</span><span class="p">)</span> <span class="p">{</span></span>
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872
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<pre style="margin: 0;">+<span id="LC872" class="line" lang="c"> <span class="n" style="color: #333;">d</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">][</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Tv</span><span class="p">;</span></span>
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803
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873
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<pre style="margin: 0;"> <span id="LC873" class="line" lang="c"> <span class="p">}</span></span>
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804
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<td class="diff-line-num new_line old" data-linenumber="874" style="width: 35px; color: rgba(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="LC804" class="line" lang="c"> <span class="n" style="color: #333;">d</span><span class="p">[</span><span class="n" style="color: #333;">i</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;">M</span><span class="p">;</span></span>
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874
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<pre style="margin: 0;">+<span id="LC874" class="line" lang="c"> <span class="n" style="color: #333;">d</span><span class="p">[</span><span class="n" style="color: #333;">i</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;">2</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">?</span> <span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">2</span><span class="p">)</span> <span class="o" style="font-weight: 600;">:</span> <span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">2</span><span class="p">)]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Ts</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC875" class="line" lang="c"> <span class="n" style="color: #333;">d</span><span class="p">[</span><span class="n" style="color: #333;">i</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;">rewards</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">M</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC876" class="line" lang="c"> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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877
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<pre style="margin: 0;">+<span id="LC877" class="line" lang="c"> <span class="n" style="color: #333;">d</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;">d</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">5</span><span class="p">;</span></span>
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878
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<pre style="margin: 0;"> <span id="LC878" class="line" lang="c"> <span class="p">}</span></span>
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806
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<pre style="margin: 0;">-<span id="LC806" class="line" lang="c"> <span class="n" style="color: #333;">d</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">smalloc</span><span class="p">(</span><span class="mi" style="color: #099;">5</span> <span class="o" style="font-weight: 600;">*</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">));</span></span>
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807
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<pre style="margin: 0;">-<span id="LC807" 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="mi" style="color: #099;">5</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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808
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<pre style="margin: 0;">-<span id="LC808" class="line" lang="c"> <span class="n" style="color: #333;">d</span><span class="p">[</span><span class="mi" style="color: #099;">4</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;">U</span><span class="p">;</span></span>
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809
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<pre style="margin: 0;">-<span id="LC809" class="line" lang="c"> <span class="n" style="color: #333;">d</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">][</span><span class="mi" style="color: #099;">4</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">U</span><span class="p">;</span></span>
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879
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<pre style="margin: 0;">+<span id="LC879" class="line" lang="c"> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">5</span><span class="p">;</span></span>
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880
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<pre style="margin: 0;">+<span id="LC880" class="line" lang="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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881
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<pre style="margin: 0;">+<span id="LC881" class="line" lang="c"> <span class="n" style="color: #333;">d</span><span class="p">[</span><span class="mi" style="color: #099;">4</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;">rewards</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Mn</span><span class="p">;</span></span>
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810
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882
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<pre style="margin: 0;"> <span id="LC882" class="line" lang="c"> <span class="p">}</span></span>
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811
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883
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<pre style="margin: 0;"> <span id="LC883" class="line" lang="c"> <span class="n" style="color: #333;">d</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">][</span><span class="mi" style="color: #099;">4</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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812
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<pre style="margin: 0;">-<span id="LC812" class="line" lang="c"> <span class="n" style="color: #333;">rewards</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;">Penalties</span><span class="p">));</span></span>
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813
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884
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<pre style="margin: 0;"> <span id="LC884" class="line" lang="c"> <span class="n" style="color: #333;">rewards</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">d</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">**</span><span class="p">)</span> <span class="n" style="color: #333;">d</span><span class="p">;</span></span>
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814
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<pre style="margin: 0;">-<span id="LC814" class="line" lang="c"> <span class="n" style="color: #333;">rewards</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">W1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">W1</span><span class="p">;</span></span>
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815
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<pre style="margin: 0;">-<span id="LC815" class="line" lang="c"> <span class="n" style="color: #333;">rewards</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">U</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">U</span><span class="p">;</span></span>
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816
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<pre style="margin: 0;">-<span id="LC816" class="line" lang="c"> <span class="n" style="color: #333;">rewards</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">M</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">M</span><span class="p">;</span></span>
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817
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<pre style="margin: 0;">-<span id="LC817" class="line" lang="c"> <span class="n" style="color: #333;">rewards</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">MM</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">MM</span><span class="p">;</span></span>
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818
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<pre style="margin: 0;">-<span id="LC818" class="line" lang="c"> <span class="n" style="color: #333;">rewards</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">PE</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">PE</span><span class="p">;</span></span>
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819
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885
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<pre style="margin: 0;"> <span id="LC885" class="line" lang="c"> </span>
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820
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886
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<pre style="margin: 0;"> <span id="LC886" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">spltDB</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">targetNum</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="p">{</span></span>
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821
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887
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<pre style="margin: 0;"> <span id="LC887" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* allocate space for commands */</span></span>
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<td class="diff-line-num unfold js-unfold old_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="diff-line-num unfold js-unfold new_line" data-linenumber="893" style="width: 35px; color: rgba(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">@@ -827,8 +893,8 @@ int kma_main(int argc, char *argv[]) {</td>
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827
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893
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<pre style="margin: 0;"> <span id="LC893" 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;">escape</span><span class="p">)</span> <span class="p">{</span></span>
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828
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894
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<pre style="margin: 0;"> <span id="LC894" class="line" lang="c"> <span class="n" style="color: #333;">size</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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829
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895
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<pre style="margin: 0;"> <span id="LC895" class="line" lang="c"> <span class="p">}</span></span>
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830
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<pre style="margin: 0;">-<span id="LC830" 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;">strlen</span><span class="p">(</span><span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="n" style="color: #333;"><span class="idiff left right">i</span></span><span class="p">]);</span></span>
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831
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<pre style="margin: 0;">-<span id="LC831" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">strncmp</span><span class="p">(</span><span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="n" style="color: #333;"><span class="idiff left right">i</span></span><span class="p">],</span> <span class="s" style="color: #d14;">"-i"</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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896
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<pre style="margin: 0;">+<span id="LC896" class="line" lang="c"> <span class="n" style="color: #333;">size</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;">argv</span><span class="p">[</span><span class="n" style="color: #333;"><span class="idiff left right">args</span></span><span class="p">]);</span></span>
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897
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<pre style="margin: 0;">+<span id="LC897" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">strncmp</span><span class="p">(</span><span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="n" style="color: #333;"><span class="idiff left right">args</span></span><span class="p">],</span> <span class="s" style="color: #d14;">"-i"</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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832
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898
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<pre style="margin: 0;"> <span id="LC898" class="line" lang="c"> <span class="n" style="color: #333;">escape</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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833
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899
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<pre style="margin: 0;"> <span id="LC899" class="line" lang="c"> <span class="p">}</span></span>
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834
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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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<li id="57966272a58cfa0f29a50e15609a883267e2471e">
<a href="https://salsa.debian.org/med-team/kma/commit/f5137c3d39949889292033da254f861b4981ebbf#57966272a58cfa0f29a50e15609a883267e2471e"><strong>loadupdate.c</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="148" style="width: 35px; color: rgba(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="148" style="width: 35px; color: rgba(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">@@ -148,17 +148,15 @@ unsigned ** hashMapKMA_openValues(HashMapKMA *src) {</td>
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148
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148
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<pre style="margin: 0;"> <span id="LC148" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">Values</span><span class="p">;</span></span>
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149
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149
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<pre style="margin: 0;"> <span id="LC149" class="line" lang="c"><span class="p">}</span></span>
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150
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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="n" style="color: #333;"><span class="idiff left">HashMapKMA</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="nf" style="color: #900; font-weight: 600;"><span class="idiff">load_DBs</span></span><span class="p"><span class="idiff">(</span></span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">char</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="n" style="color: #333;"><span class="idiff">templatefilename</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">char</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="n" style="color: #333;"><span class="idiff">outputfilename</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">unsigned</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">**</span></span><span class="n" style="color: #333;"><span class="idiff">template_lengths</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">unsigned</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">**</span></span><span class="n" style="color: #333;"><span class="idiff">template_ulengths</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">unsigned</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">**</span></span><span class="n" style="color: #333;"><span class="idiff right">template_slengths</span></span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">unsigned</span></span><span class="idiff"> </span><span class="nf" style="color: #900; font-weight: 600;"><span class="idiff">load_DBs</span></span><span class="p"><span class="idiff">(</span></span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">char</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="n" style="color: #333;"><span class="idiff">templatefilename</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">char</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="n" style="color: #333;"><span class="idiff">outputfilename</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">unsigned</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">**</span></span><span class="n" style="color: #333;"><span class="idiff">template_lengths</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">unsigned</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">**</span></span><span class="n" style="color: #333;"><span class="idiff">template_ulengths</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">unsigned</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">**</span></span><span class="n" style="color: #333;"><span class="idiff">template_slengths</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">HashMapKMA</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="n" style="color: #333;"><span class="idiff right">finalDB</span></span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC152" class="line" lang="c"> </span>
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<pre style="margin: 0;">-<span id="LC153" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">file_len</span><span class="p">,</span> <span class="n" style="color: #333;">out_len</span><span class="p">,</span> <span class="n" style="color: #333;">DB_size</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">file_len</span><span class="p">,</span> <span class="n" style="color: #333;">out_len</span><span class="p">,</span> <span class="n" style="color: #333;">DB_size</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">kmerindex</span></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="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">infile</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC155" 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;">finalDB</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC155" class="line" lang="c"> </span>
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157
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<pre style="margin: 0;"> <span id="LC156" class="line" lang="c"> <span class="n" style="color: #333;">file_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;">templatefilename</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC157" class="line" lang="c"> <span class="n" style="color: #333;">out_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;">outputfilename</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC158" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC159" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* load hash */</span></span>
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<pre style="margin: 0;">-<span id="LC161" class="line" lang="c"> <span class="n" style="color: #333;">finalDB</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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162
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<pre style="margin: 0;"> <span id="LC160" class="line" lang="c"> <span class="n" style="color: #333;">strcat</span><span class="p">(</span><span class="n" style="color: #333;">templatefilename</span><span class="p">,</span> <span class="s" style="color: #d14;">".comp.b"</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC161" class="line" lang="c"> <span class="n" style="color: #333;">infile</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;">templatefilename</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="LC162" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">hashMapKMAload</span><span class="p">(</span><span class="n" style="color: #333;">finalDB</span><span class="p">,</span> <span class="n" style="color: #333;">infile</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="178" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -178,13 +176,14 @@ HashMapKMA * load_DBs(char *templatefilename, char *outputfilename, unsigned **t</td>
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178
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<pre style="margin: 0;"> <span id="LC176" class="line" lang="c"> <span class="p">}</span></span>
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179
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<pre style="margin: 0;"> <span id="LC177" class="line" lang="c"> <span class="n" style="color: #333;">templatefilename</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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180
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<pre style="margin: 0;"> <span id="LC178" class="line" lang="c"> <span class="n" style="color: #333;">fread</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">DB_size</span><span class="p">,</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span><span class="p">),</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">infile</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC181" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">finalDB</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">prefix<span class="idiff left right">_len</span></span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">finalDB</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">prefix</span><span class="p">)</span> <span class="p">{</span></span>
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182
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180
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<pre style="margin: 0;"> <span id="LC180" class="line" lang="c"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">template_lengths</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;">DB_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="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span><span class="p">));</span></span>
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183
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181
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<pre style="margin: 0;"> <span id="LC181" class="line" lang="c"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">template_slengths</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;">DB_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="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span><span class="p">));</span></span>
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184
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182
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<pre style="margin: 0;"> <span id="LC182" class="line" lang="c"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">template_ulengths</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;">DB_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="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span><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 class="n" style="color: #333;">fread</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">template_lengths</span><span class="p">,</span> <span class="k" style="font-weight: 600;">sizeof</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;">DB_size</span><span class="p">,</span> <span class="n" style="color: #333;">infile</span><span class="p">);</span></span>
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185
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184
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<pre style="margin: 0;"> <span id="LC184" class="line" lang="c"> <span class="n" style="color: #333;">fread</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">template_slengths</span><span class="p">,</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span><span class="p">),</span> <span class="n" style="color: #333;">DB_size</span><span class="p">,</span> <span class="n" style="color: #333;">infile</span><span class="p">);</span></span>
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186
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<td class="diff-line-num new_line" data-linenumber="185" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
185
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<pre style="margin: 0;"> <span id="LC185" class="line" lang="c"> <span class="n" style="color: #333;">fread</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">template_ulengths</span><span class="p">,</span> <span class="k" style="font-weight: 600;">sizeof</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;">DB_size</span><span class="p">,</span> <span class="n" style="color: #333;">infile</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="n" style="color: #333;"><span class="idiff left">fread</span></span><span class="p"><span class="idiff">(</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="n" style="color: #333;"><span class="idiff">template_lengths</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">sizeof</span></span><span class="p"><span class="idiff">(</span></span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">unsigned</span></span><span class="p"><span class="idiff">),</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">DB_size</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">infile</span></span><span class="p"><span class="idiff right">)</span>;</span></span>
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186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="c"> <span class="n" style="color: #333;"><span class="idiff left">kmerindex</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">**</span></span><span class="n" style="color: #333;"><span class="idiff right">template_slengths</span></span><span class="p">;</span></span>
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188
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187
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<pre style="margin: 0;"> <span id="LC187" class="line" lang="c"> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">template_ulengths</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="mi" style="color: #099;">1</span><span class="p">;</span></span>
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189
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188
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<pre style="margin: 0;"> <span id="LC188" class="line" lang="c"> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">template_slengths</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="mi" style="color: #099;">1</span><span class="p">;</span></span>
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190
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189
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<pre style="margin: 0;"> <span id="LC189" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="192" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="191" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -192,6 +191,7 @@ HashMapKMA * load_DBs(char *templatefilename, char *outputfilename, unsigned **t</td>
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192
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191
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<pre style="margin: 0;"> <span id="LC191" class="line" lang="c"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">template_slengths</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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193
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192
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<pre style="margin: 0;"> <span id="LC192" class="line" lang="c"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">template_ulengths</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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194
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193
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<pre style="margin: 0;"> <span id="LC193" class="line" lang="c"> <span class="n" style="color: #333;">fread</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">template_lengths</span><span class="p">,</span> <span class="k" style="font-weight: 600;">sizeof</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;">DB_size</span><span class="p">,</span> <span class="n" style="color: #333;">infile</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="194" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
194
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="c"> <span class="n" style="color: #333;">kmerindex</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">template_lengths</span><span class="p">;</span></span>
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195
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195
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<pre style="margin: 0;"> <span id="LC195" class="line" lang="c"> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">template_lengths</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="mi" style="color: #099;">1</span><span class="p">;</span></span>
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196
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196
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<pre style="margin: 0;"> <span id="LC196" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC197" class="line" lang="c"> <span class="n" style="color: #333;">fclose</span><span class="p">(</span><span class="n" style="color: #333;">infile</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">@@ -222,5 +222,5 @@ HashMapKMA * load_DBs(char *templatefilename, char *outputfilename, unsigned **t</td>
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<pre style="margin: 0;"> <span id="LC222" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC223" class="line" lang="c"> <span class="n" style="color: #333;">templatefilename</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="LC224" class="line" lang="c"> </span>
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<pre style="margin: 0;">-<span id="LC225" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;"><span class="idiff left right">finalDB</span></span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;"><span class="idiff left right">kmerindex</span></span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC226" class="line" lang="c"><span class="p">}</span></span></pre>
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<a href="https://salsa.debian.org/med-team/kma/commit/f5137c3d39949889292033da254f861b4981ebbf#9f42ead3b08d7f8ac36940bb98a4415aa62390dd"><strong>loadupdate.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">@@ -24,4 +24,4 @@ void * memdup(const void * src, size_t size);</td>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">CP</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">templatefilename</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">outputfilename</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="c"><span class="n" style="color: #333;">HashMap</span> <span class="o" style="font-weight: 600;">*</span> <span class="nf" style="color: #900; font-weight: 600;">hashMapKMA_openChains</span><span class="p">(</span><span class="n" style="color: #333;">HashMapKMA</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">src</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC26" 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="nf" style="color: #900; font-weight: 600;">hashMapKMA_openValues</span><span class="p">(</span><span class="n" style="color: #333;">HashMapKMA</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">src</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="c"><span class="n" style="color: #333;"><span class="idiff left">HashMapKMA</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="nf" style="color: #900; font-weight: 600;"><span class="idiff">load_DBs</span></span><span class="p"><span class="idiff">(</span></span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">char</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="n" style="color: #333;"><span class="idiff">templatefilename</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">char</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="n" style="color: #333;"><span class="idiff">outputfilename</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">unsigned</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">**</span></span><span class="n" style="color: #333;"><span class="idiff">template_lengths</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">unsigned</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">**</span></span><span class="n" style="color: #333;"><span class="idiff">template_ulengths</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">unsigned</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">**</span></span><span class="n" style="color: #333;"><span class="idiff right">template_slengths</span></span><span class="p">);</span></span></pre>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">unsigned</span></span><span class="idiff"> </span><span class="nf" style="color: #900; font-weight: 600;"><span class="idiff">load_DBs</span></span><span class="p"><span class="idiff">(</span></span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">char</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="n" style="color: #333;"><span class="idiff">templatefilename</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">char</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="n" style="color: #333;"><span class="idiff">outputfilename</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">unsigned</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">**</span></span><span class="n" style="color: #333;"><span class="idiff">template_lengths</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">unsigned</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">**</span></span><span class="n" style="color: #333;"><span class="idiff">template_ulengths</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">unsigned</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">**</span></span><span class="n" style="color: #333;"><span class="idiff">template_slengths</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">HashMapKMA</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="n" style="color: #333;"><span class="idiff right">finalDB</span></span><span class="p">);</span></span></pre>
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<a href="https://salsa.debian.org/med-team/kma/commit/f5137c3d39949889292033da254f861b4981ebbf#e54b00420aceec6f11948d8c279380a68b99ba52"><strong>makeindex.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">@@ -71,7 +71,6 @@ void makeDB(HashMap *templates, int kmerindex, char **inputfiles, int fileCount,</td>
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="c"> <span class="n" style="color: #333;">seq_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;">"wb"</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC72" 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="LC73" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC74" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">dumpIndex</span> <span class="o" style="font-weight: 600;">==</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">makeIndexing</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="76" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">appender</span><span class="p">)</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;">strcat</span><span class="p">(</span><span class="n" style="color: #333;">outputfilename</span><span class="p">,</span> <span class="s" style="color: #d14;">".index.b"</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -109,16 +108,16 @@ void makeDB(HashMap *templates, int kmerindex, char **inputfiles, int fileCount,</td>
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109
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108
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<pre style="margin: 0;"> <span id="LC108" class="line" lang="c"> <span class="k" style="font-weight: 600;">while</span><span class="p">(</span><span class="n" style="color: #333;">isspace</span><span class="p">(</span><span class="o" style="font-weight: 600;">*--</span><span class="n" style="color: #333;">seq</span><span class="p">))</span> <span class="p">{</span></span>
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110
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109
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<pre style="margin: 0;"> <span id="LC109" class="line" lang="c"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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111
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110
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<pre style="margin: 0;"> <span id="LC110" class="line" lang="c"> <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>
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113
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111
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<pre style="margin: 0;"> <span id="LC111" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</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="p">{</span></span>
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114
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<td class="diff-line-num new_line" data-linenumber="112" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
112
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<pre style="margin: 0;"> <span id="LC112" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">name_out</span><span class="p">,</span> <span class="s" style="color: #d14;">"%s B%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;">header</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">bias</span><span class="p">);</span></span>
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115
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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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116
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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;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">name_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="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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117
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115
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<pre style="margin: 0;"> <span id="LC115" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
118
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<td class="diff-line-num new_line" data-linenumber="116" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
116
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<pre style="margin: 0;"> <span id="LC116" class="line" lang="c"> <span class="n" style="color: #333;">updateAnnotsPtr</span><span class="p">(</span><span class="n" style="color: #333;">compressor</span><span class="p">,</span> <span class="n" style="color: #333;">templates</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">DB_size</span><span class="p">,</span> <span class="n" style="color: #333;">kmerindex</span><span class="p">,</span> <span class="n" style="color: #333;">seq_out</span><span class="p">,</span> <span class="n" style="color: #333;">index_out</span><span class="p">,</span> <span class="n" style="color: #333;">template_lengths</span><span class="p">,</span> <span class="n" style="color: #333;">template_ulengths</span><span class="p">,</span> <span class="n" style="color: #333;">template_slengths</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="117" style="width: 35px; color: rgba(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="LC117" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* here */</span></span>
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119
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118
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<pre style="margin: 0;"> <span id="LC118" 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;">"# Added:</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;">header</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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120
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<pre style="margin: 0;"> <span id="LC119" class="line" lang="c"> </span>
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<pre style="margin: 0;">-<span id="LC121" 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;"><span class="idiff left">templates</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff right">DB_size</span></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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<td class="diff-line-num new new_line" data-linenumber="120" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
120
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<pre style="margin: 0;">+<span id="LC120" 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="p"><span class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">templates</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">DB_size</span></span><span class="p"><span class="idiff right">)</span></span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">USHRT_MAX</span><span class="p">)</span> <span class="p">{</span></span>
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122
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<pre style="margin: 0;"> <span id="LC121" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* convert values to unsigned */</span></span>
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<pre style="margin: 0;"> <span id="LC122" class="line" lang="c"> <span class="n" style="color: #333;">convertToU</span><span class="p">(</span><span class="n" style="color: #333;">templates</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC123" class="line" lang="c"> <span class="p">}</span></span>
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<a href="https://salsa.debian.org/med-team/kma/commit/f5137c3d39949889292033da254f861b4981ebbf#ace9d341f8ce5776855494d2885e4a314493ec78"><strong>penalties.h</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -21,10 +21,12 @@</td>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="c"><span class="k" style="font-weight: 600;">typedef</span> <span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">penalties</span> <span class="n" style="color: #333;">Penalties</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="c"><span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">penalties</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">d</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">W1</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">U</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">M</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">MM</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">U</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">W1</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">Wl</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">Mn</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">PE</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="c"><span class="p">};</span></span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span></pre>
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<a href="https://salsa.debian.org/med-team/kma/commit/f5137c3d39949889292033da254f861b4981ebbf#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">@@ -43,6 +43,7 @@</td>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "sam.h"</span></span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "stdnuc.h"</span></span>
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<pre style="margin: 0;"> <span id="LC45" 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="LC46" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "tmp.h"</span></span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "updatescores.h"</span></span>
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48
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "vcf.h"</span></span>
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48
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49
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifndef _WIN32</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">@@ -254,7 +255,7 @@ int runKMA(char *templatefilename, char *outputfilename, char *exePrev, int ConC</td>
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254
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255
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<pre style="margin: 0;"> <span id="LC255" 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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255
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256
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<pre style="margin: 0;"> <span id="LC256" 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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256
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257
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<pre style="margin: 0;"> <span id="LC257" class="line" lang="c"> <span class="p">}</span></span>
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257
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<pre style="margin: 0;">-<span id="LC257" class="line" lang="c"> <span class="n" style="color: #333;">frag_out_raw</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tmp<span class="idiff left">file</span></span><span class="p"><span class="idiff right">(</span>);</span></span>
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258
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<pre style="margin: 0;">+<span id="LC258" class="line" lang="c"> <span class="n" style="color: #333;">frag_out_raw</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tmp<span class="idiff left">F</span></span><span class="p"><span class="idiff">(</span></span><span class="mi" style="color: #099;"><span class="idiff right">0</span></span><span class="p">);</span></span>
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258
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259
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<pre style="margin: 0;"> <span id="LC259" 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;">frag_out_raw</span><span class="p">)</span> <span class="p">{</span></span>
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259
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260
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<pre style="margin: 0;"> <span id="LC260" class="line" lang="c"> <span class="n" style="color: #333;">ERROR</span><span class="p">();</span></span>
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260
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261
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<pre style="margin: 0;"> <span id="LC261" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1394" style="width: 35px; color: rgba(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="1395" style="width: 35px; color: rgba(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">@@ -1394,7 +1395,7 @@ int runKMA_MEM(char *templatefilename, char *outputfilename, char *exePrev, int</td>
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1394
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1395
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<pre style="margin: 0;"> <span id="LC1395" 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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1396
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<pre style="margin: 0;"> <span id="LC1396" 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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1396
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1397
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<pre style="margin: 0;"> <span id="LC1397" class="line" lang="c"> <span class="p">}</span></span>
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1397
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<pre style="margin: 0;">-<span id="LC1397" class="line" lang="c"> <span class="n" style="color: #333;">frag_out_raw</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tmp<span class="idiff left">file</span></span><span class="p"><span class="idiff right">(</span>);</span></span>
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1398
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<pre style="margin: 0;">+<span id="LC1398" class="line" lang="c"> <span class="n" style="color: #333;">frag_out_raw</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tmp<span class="idiff left">F</span></span><span class="p"><span class="idiff">(</span></span><span class="mi" style="color: #099;"><span class="idiff right">0</span></span><span class="p">);</span></span>
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1398
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1399
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<pre style="margin: 0;"> <span id="LC1399" 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;">frag_out_raw</span><span class="p">)</span> <span class="p">{</span></span>
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1399
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1400
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<pre style="margin: 0;"> <span id="LC1400" class="line" lang="c"> <span class="n" style="color: #333;">ERROR</span><span class="p">();</span></span>
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1400
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1401
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<pre style="margin: 0;"> <span id="LC1401" class="line" lang="c"> <span class="p">}</span></span>
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<li id="f9ead8e7fb7b1680f786604627e0ac2147f4b7ef">
<a href="https://salsa.debian.org/med-team/kma/commit/f5137c3d39949889292033da254f861b4981ebbf#f9ead8e7fb7b1680f786604627e0ac2147f4b7ef"><strong>savekmers.c</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="393" style="width: 35px; color: rgba(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="393" style="width: 35px; color: rgba(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">@@ -393,17 +393,13 @@ int getProxiMatchSparse(int *bestTemplates, int *Score, int kmersize, int n_kmer</td>
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393
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<pre style="margin: 0;"> <span id="LC393" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">bestScore</span><span class="p">;</span></span>
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394
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394
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<pre style="margin: 0;"> <span id="LC394" class="line" lang="c"><span class="p">}</span></span>
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395
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395
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<pre style="margin: 0;"> <span id="LC395" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC396" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">clearScore</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">bestTemplates</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">Score</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC396" class="line" lang="c"><span class="k" style="font-weight: 600;"><span class="idiff left">static</span></span><span class="idiff right"> </span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">clearScore</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">bestTemplates</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">Score</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC397" class="line" lang="c"> </span>
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398
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398
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<pre style="margin: 0;"> <span id="LC398" 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>
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399
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399
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<pre style="margin: 0;"> <span id="LC399" class="line" lang="c"> </span>
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400
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400
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<pre style="margin: 0;"> <span id="LC400" 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;">bestTemplates</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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401
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401
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<pre style="margin: 0;"> <span id="LC401" class="line" lang="c"> <span class="k" style="font-weight: 600;">while</span><span class="p">(</span><span class="o" style="font-weight: 600;">--</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="p">{</span></span>
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402
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402
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<pre style="margin: 0;"> <span id="LC402" class="line" lang="c"> <span class="n" style="color: #333;">Score</span><span class="p">[</span><span class="o" style="font-weight: 600;">*++</span><span class="n" style="color: #333;">bestTemplates</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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403
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<pre style="margin: 0;">-<span id="LC403" 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;">bestTemplates</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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404
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<pre style="margin: 0;">-<span id="LC404" 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;">"Moher fucker.</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="LC405" 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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<pre style="margin: 0;">-<span id="LC406" class="line" lang="c"> <span class="p">}</span></span>
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403
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<pre style="margin: 0;"> <span id="LC403" class="line" lang="c"> <span class="p">}</span></span>
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404
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<pre style="margin: 0;"> <span id="LC404" class="line" lang="c"> </span>
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409
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405
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<pre style="margin: 0;"> <span id="LC405" 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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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4759" style="width: 35px; color: rgba(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="4755" style="width: 35px; color: rgba(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">@@ -4759,3 +4755,299 @@ void ankerAndClean_MEM(int *regionTemplates, int *Score, int *Score_r, char *inc</td>
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4759
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4755
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<pre style="margin: 0;"> <span id="LC4755" class="line" lang="c"> <span class="n" style="color: #333;">header</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seq</span><span class="p">[</span><span class="n" style="color: #333;">l</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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4760
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4756
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<pre style="margin: 0;"> <span id="LC4756" class="line" lang="c"> <span class="n" style="color: #333;">header</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">l</span><span class="p">;</span></span>
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4761
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4757
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<pre style="margin: 0;"> <span id="LC4757" class="line" lang="c"><span class="p">}</span></span>
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4758
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<pre style="margin: 0;">+<span id="LC4758" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC4759" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">save_kmers_chain</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">HashMapKMA</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">templates</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Penalties</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">rewards</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">bestTemplates</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">bestTemplates_r</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">Score</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">Score_r</span><span class="p">,</span> <span class="n" style="color: #333;">CompDNA</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq</span><span class="p">,</span> <span class="n" style="color: #333;">CompDNA</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq_r</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Qseqs</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">header</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">extendScore</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">exhaustive</span><span class="p">,</span> <span class="k" style="font-weight: 600;">volatile</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">excludeOut</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">out</span><span class="p">)</span> <span class="p">{</span></span>
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4760
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<pre style="margin: 0;">+<span id="LC4760" class="line" lang="c"> </span>
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<td class="diff-line-num new new_line" data-linenumber="4761" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4761
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<pre style="margin: 0;">+<span id="LC4761" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* return 0 for match, 1 otherwise */</span></span>
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4762
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<pre style="margin: 0;">+<span id="LC4762" class="line" lang="c"> <span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">Sizes</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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4763
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<pre style="margin: 0;">+<span id="LC4763" class="line" lang="c"> <span class="k" style="font-weight: 600;">static</span> <span class="n" style="color: #333;">KmerAnker</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">tVF_scores</span><span class="p">,</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">tVR_scores</span><span class="p">;</span></span>
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4764
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<pre style="margin: 0;">+<span id="LC4764" class="line" lang="c"> </span>
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<td class="diff-line-num new new_line" data-linenumber="4765" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4765
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<pre style="margin: 0;">+<span id="LC4765" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">Wl</span><span class="p">,</span> <span class="n" style="color: #333;">W1</span><span class="p">,</span> <span class="n" style="color: #333;">U</span><span class="p">,</span> <span class="n" style="color: #333;">M</span><span class="p">,</span> <span class="n" style="color: #333;">MM</span><span class="p">,</span> <span class="n" style="color: #333;">Ms</span><span class="p">,</span> <span class="n" style="color: #333;">MMs</span><span class="p">,</span> <span class="n" style="color: #333;">Us</span><span class="p">,</span> <span class="n" style="color: #333;">W1s</span><span class="p">,</span> <span class="n" style="color: #333;">score</span><span class="p">,</span> <span class="n" style="color: #333;">gaps</span><span class="p">,</span> <span class="n" style="color: #333;">template</span><span class="p">,</span> <span class="n" style="color: #333;">maxS</span><span class="p">;</span></span>
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4766
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<pre style="margin: 0;">+<span id="LC4766" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">bests</span><span class="p">;</span></span>
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4767
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<pre style="margin: 0;">+<span id="LC4767" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">j</span><span class="p">,</span> <span class="n" style="color: #333;">rc</span><span class="p">,</span> <span class="n" style="color: #333;">shifter</span><span class="p">,</span> <span class="n" style="color: #333;">kmersize</span><span class="p">,</span> <span class="n" style="color: #333;">DB_size</span><span class="p">,</span> <span class="n" style="color: #333;">SU</span><span class="p">,</span> <span class="n" style="color: #333;">HIT</span><span class="p">,</span> <span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="n" style="color: #333;">end</span><span class="p">,</span> <span class="n" style="color: #333;">pos</span><span class="p">;</span></span>
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4768
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<pre style="margin: 0;">+<span id="LC4768" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">hitCounter</span><span class="p">,</span> <span class="n" style="color: #333;">hitCounter_r</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4769" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4769
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<pre style="margin: 0;">+<span id="LC4769" 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;">last</span><span class="p">;</span></span>
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4770
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<pre style="margin: 0;">+<span id="LC4770" 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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4771
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<pre style="margin: 0;">+<span id="LC4771" 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;">include</span><span class="p">;</span></span>
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4772
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<pre style="margin: 0;">+<span id="LC4772" class="line" lang="c"> <span class="n" style="color: #333;">CompDNA</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseqP</span><span class="p">;</span></span>
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4773
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<pre style="margin: 0;">+<span id="LC4773" class="line" lang="c"> <span class="n" style="color: #333;">KmerAnker</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">V_score</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">V_scores</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">VF_scores</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">VR_scores</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">tmp_score</span><span class="p">;</span></span>
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4774
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<pre style="margin: 0;">+<span id="LC4774" class="line" lang="c"> </span>
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<td class="diff-line-num new new_line" data-linenumber="4775" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4775
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<pre style="margin: 0;">+<span id="LC4775" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">qseq</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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4776
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<pre style="margin: 0;">+<span id="LC4776" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">Sizes</span><span class="p">)</span> <span class="p">{</span></span>
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4777
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<pre style="margin: 0;">+<span id="LC4777" class="line" lang="c"> <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">Sizes</span><span class="p">);</span></span>
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4778
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<pre style="margin: 0;">+<span id="LC4778" class="line" lang="c"> <span class="n" style="color: #333;">Sizes</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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4779
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<pre style="margin: 0;">+<span id="LC4779" 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;">bestTemplates</span><span class="p">;</span></span>
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4780
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<pre style="margin: 0;">+<span id="LC4780" 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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<td class="diff-line-num new new_line" data-linenumber="4781" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4781
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<pre style="margin: 0;">+<span id="LC4781" class="line" lang="c"> <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">tVF_scores</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]);</span></span>
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4782
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<pre style="margin: 0;">+<span id="LC4782" class="line" lang="c"> <span class="p">}</span></span>
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4783
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<pre style="margin: 0;">+<span id="LC4783" class="line" lang="c"> <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">tVF_scores</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4784" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4784
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<pre style="margin: 0;">+<span id="LC4784" 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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4785
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<pre style="margin: 0;">+<span id="LC4785" 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;">bestTemplates</span><span class="p">;</span></span>
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4786
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<pre style="margin: 0;">+<span id="LC4786" class="line" lang="c"> <span class="n" style="color: #333;">Sizes</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;">i</span> <span class="o" style="font-weight: 600;">*</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">));</span></span>
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4787
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<pre style="margin: 0;">+<span id="LC4787" class="line" lang="c"> <span class="n" style="color: #333;">tVF_scores</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">smalloc</span><span class="p">(</span><span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">*</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">KmerAnker</span> <span class="o" style="font-weight: 600;">*</span><span class="p">));</span></span>
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4788
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<pre style="margin: 0;">+<span id="LC4788" class="line" lang="c"> <span class="n" style="color: #333;">tVR_scores</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tVF_scores</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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4789
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<pre style="margin: 0;">+<span id="LC4789" 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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<td class="diff-line-num new new_line" data-linenumber="4790" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4790
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<pre style="margin: 0;">+<span id="LC4790" class="line" lang="c"> <span class="n" style="color: #333;">Sizes</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;">256</span><span class="p">;</span></span>
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4791
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<pre style="margin: 0;">+<span id="LC4791" class="line" lang="c"> <span class="n" style="color: #333;">tVF_scores</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">calloc</span><span class="p">(</span><span class="mi" style="color: #099;">512</span><span class="p">,</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">KmerAnker</span><span class="p">));</span></span>
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4792
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<pre style="margin: 0;">+<span id="LC4792" 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;">tVF_scores</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">])</span> <span class="p">{</span></span>
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4793
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<pre style="margin: 0;">+<span id="LC4793" class="line" lang="c"> <span class="n" style="color: #333;">ERROR</span><span class="p">();</span></span>
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4794
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<pre style="margin: 0;">+<span id="LC4794" 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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4795
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<pre style="margin: 0;">+<span id="LC4795" class="line" lang="c"> <span class="n" style="color: #333;">tVR_scores</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tVF_scores</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">256</span><span class="p">;</span></span>
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4796
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<pre style="margin: 0;">+<span id="LC4796" class="line" lang="c"> <span class="p">}</span></span>
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4797
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<pre style="margin: 0;">+<span id="LC4797" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4798" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4798
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<pre style="margin: 0;">+<span id="LC4798" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4799" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4799
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<pre style="margin: 0;">+<span id="LC4799" 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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<td class="diff-line-num new new_line" data-linenumber="4800" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4800
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<pre style="margin: 0;">+<span id="LC4800" 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;">qseq</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seqlen</span> <span class="o" style="font-weight: 600;"><</span> <span class="p">(</span><span class="n" style="color: #333;">kmersize</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;">kmersize</span><span class="p">))</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4801" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4801
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<pre style="margin: 0;">+<span id="LC4801" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</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="4802" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4802
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<pre style="margin: 0;">+<span id="LC4802" 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;">DB_size</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">templates</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">DB_size</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">USHRT_MAX</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4803" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4803
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<pre style="margin: 0;">+<span id="LC4803" class="line" lang="c"> <span class="n" style="color: #333;">SU</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="4804" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4804
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<pre style="margin: 0;">+<span id="LC4804" 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="4805" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4805
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<pre style="margin: 0;">+<span id="LC4805" class="line" lang="c"> <span class="n" style="color: #333;">SU</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="4806" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4806
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<pre style="margin: 0;">+<span id="LC4806" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4807" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4807
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<pre style="margin: 0;">+<span id="LC4807" class="line" lang="c"> <span class="n" style="color: #333;">shifter</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</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="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="4808" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4808
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<pre style="margin: 0;">+<span id="LC4808" class="line" lang="c"> <span class="n" style="color: #333;">M</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rewards</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">M</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4809" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4809
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<pre style="margin: 0;">+<span id="LC4809" class="line" lang="c"> <span class="n" style="color: #333;">MM</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rewards</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">MM</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4810" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4810
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<pre style="margin: 0;">+<span id="LC4810" class="line" lang="c"> <span class="n" style="color: #333;">U</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rewards</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">U</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4811" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4811
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<pre style="margin: 0;">+<span id="LC4811" class="line" lang="c"> <span class="n" style="color: #333;">W1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rewards</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">W1</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4812" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4812
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<pre style="margin: 0;">+<span id="LC4812" class="line" lang="c"> <span class="n" style="color: #333;">Wl</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rewards</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Wl</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4813" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4813
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<pre style="margin: 0;">+<span id="LC4813" class="line" lang="c"> <span class="n" style="color: #333;">include</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="p">)</span> <span class="p">(</span><span class="n" style="color: #333;">extendScore</span> <span class="o" style="font-weight: 600;">+</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="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="4814" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4814
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<pre style="margin: 0;">+<span id="LC4814" class="line" lang="c"> <span class="n" style="color: #333;">hitCounter</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="4815" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4815
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<pre style="margin: 0;">+<span id="LC4815" class="line" lang="c"> <span class="n" style="color: #333;">hitCounter_r</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="4816" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4816
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<pre style="margin: 0;">+<span id="LC4816" 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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<td class="diff-line-num new new_line" data-linenumber="4817" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4817
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<pre style="margin: 0;">+<span id="LC4817" 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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4818
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<pre style="margin: 0;">+<span id="LC4818" class="line" lang="c"> </span>
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<td class="diff-line-num new new_line" data-linenumber="4819" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4819
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<pre style="margin: 0;">+<span id="LC4819" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">Sizes</span><span class="p">[</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">Score</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">qseq</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">size</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4820" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4820
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<pre style="margin: 0;">+<span id="LC4820" class="line" lang="c"> <span class="n" style="color: #333;">Sizes</span><span class="p">[</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">Score</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">qseq</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">size</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="4821" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4821
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<pre style="margin: 0;">+<span id="LC4821" class="line" lang="c"> <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">tVF_scores</span><span class="p">[</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">Score</span><span class="p">]);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4822" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4822
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<pre style="margin: 0;">+<span id="LC4822" class="line" lang="c"> <span class="n" style="color: #333;">tVF_scores</span><span class="p">[</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">Score</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">calloc</span><span class="p">(</span><span class="n" style="color: #333;">qseq</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">size</span><span class="p">,</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">KmerAnker</span><span class="p">));</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4823" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4823
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<pre style="margin: 0;">+<span id="LC4823" 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;">tVF_scores</span><span class="p">[</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">Score</span><span class="p">])</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4824" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4824
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<pre style="margin: 0;">+<span id="LC4824" class="line" lang="c"> <span class="n" style="color: #333;">ERROR</span><span class="p">();</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4825" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4825
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<pre style="margin: 0;">+<span id="LC4825" 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="4826" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4826
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<pre style="margin: 0;">+<span id="LC4826" class="line" lang="c"> <span class="n" style="color: #333;">tVR_scores</span><span class="p">[</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">Score</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tVF_scores</span><span class="p">[</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">Score</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">qseq</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">size</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4827" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4827
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<pre style="margin: 0;">+<span id="LC4827" class="line" lang="c"> <span class="p">}</span></span>
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4828
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<pre style="margin: 0;">+<span id="LC4828" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4829" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4829
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<pre style="margin: 0;">+<span id="LC4829" class="line" lang="c"> <span class="n" style="color: #333;">VF_scores</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tVF_scores</span><span class="p">[</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">Score</span><span class="p">];</span></span>
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4830
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<pre style="margin: 0;">+<span id="LC4830" class="line" lang="c"> <span class="n" style="color: #333;">VR_scores</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tVR_scores</span><span class="p">[</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">Score</span><span class="p">];</span></span>
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4831
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<pre style="margin: 0;">+<span id="LC4831" class="line" lang="c"> </span>
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<td class="diff-line-num new new_line" data-linenumber="4832" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4832
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<pre style="margin: 0;">+<span id="LC4832" class="line" lang="c"> <span class="n" style="color: #333;">V_scores</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">VF_scores</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4833" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4833
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<pre style="margin: 0;">+<span id="LC4833" class="line" lang="c"> <span class="n" style="color: #333;">qseqP</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">qseq</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4834" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4834
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<pre style="margin: 0;">+<span id="LC4834" class="line" lang="c"> <span class="n" style="color: #333;">rc</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4835" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4835
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<pre style="margin: 0;">+<span id="LC4835" class="line" lang="c"> <span class="k" style="font-weight: 600;">while</span><span class="p">(</span><span class="n" style="color: #333;">rc</span><span class="o" style="font-weight: 600;">--</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4836" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4836
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<pre style="margin: 0;">+<span id="LC4836" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">rc</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="4837" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4837
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<pre style="margin: 0;">+<span id="LC4837" class="line" lang="c"> <span class="n" style="color: #333;">V_scores</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">VR_scores</span><span class="p">;</span></span>
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4838
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<pre style="margin: 0;">+<span id="LC4838" class="line" lang="c"> <span class="n" style="color: #333;">qseqP</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">qseq_r</span><span class="p">;</span></span>
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4839
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<pre style="margin: 0;">+<span id="LC4839" class="line" lang="c"> <span class="n" style="color: #333;">rc_comp</span><span class="p">(</span><span class="n" style="color: #333;">qseq</span><span class="p">,</span> <span class="n" style="color: #333;">qseq_r</span><span class="p">);</span></span>
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4840
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<pre style="margin: 0;">+<span id="LC4840" class="line" lang="c"> <span class="n" style="color: #333;">hitCounter</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">hitCounter_r</span><span class="p">;</span></span>
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4841
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<pre style="margin: 0;">+<span id="LC4841" class="line" lang="c"> <span class="n" style="color: #333;">hitCounter_r</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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4842
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<pre style="margin: 0;">+<span id="LC4842" class="line" lang="c"> <span class="p">}</span></span>
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4843
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<pre style="margin: 0;">+<span id="LC4843" class="line" lang="c"> </span>
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4844
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<pre style="margin: 0;">+<span id="LC4844" class="line" lang="c"> <span class="n" style="color: #333;">HIT</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">exhaustive</span><span class="p">;</span></span>
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4845
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<pre style="margin: 0;">+<span id="LC4845" class="line" lang="c"> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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4846
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<pre style="margin: 0;">+<span id="LC4846" class="line" lang="c"> <span class="o" style="font-weight: 600;">++*</span><span class="p">(</span><span class="n" style="color: #333;">qseqP</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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4847
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<pre style="margin: 0;">+<span id="LC4847" class="line" lang="c"> <span class="n" style="color: #333;">qseqP</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">N</span><span class="p">[</span><span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">qseqP</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">N</span><span class="p">)]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">qseqP</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seqlen</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4848" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4848
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<pre style="margin: 0;">+<span id="LC4848" 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;">1</span><span class="p">;</span> <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="p">(</span><span class="n" style="color: #333;">qseqP</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">N</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">HIT</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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4849
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<pre style="margin: 0;">+<span id="LC4849" class="line" lang="c"> <span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">qseqP</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">N</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;">kmersize</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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4850
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<pre style="margin: 0;">+<span id="LC4850" class="line" lang="c"> <span class="k" style="font-weight: 600;">while</span><span class="p">(</span><span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">hashMap_get</span><span class="p">(</span><span class="n" style="color: #333;">templates</span><span class="p">,</span> <span class="n" style="color: #333;">getKmer</span><span class="p">(</span><span class="n" style="color: #333;">qseqP</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="n" style="color: #333;">j</span><span class="p">,</span> <span class="n" style="color: #333;">shifter</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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4851
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<pre style="margin: 0;">+<span id="LC4851" class="line" lang="c"> <span class="n" style="color: #333;">j</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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4852
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<pre style="margin: 0;">+<span id="LC4852" class="line" lang="c"> <span class="p">}</span></span>
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4853
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<pre style="margin: 0;">+<span id="LC4853" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">end</span><span class="p">)</span> <span class="p">{</span></span>
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4854
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<pre style="margin: 0;">+<span id="LC4854" class="line" lang="c"> <span class="n" style="color: #333;">HIT</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="4855" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4855
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<pre style="margin: 0;">+<span id="LC4855" 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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4856
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<pre style="margin: 0;">+<span id="LC4856" class="line" lang="c"> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">qseqP</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">N</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;">1</span><span class="p">;</span></span>
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4857
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<pre style="margin: 0;">+<span id="LC4857" class="line" lang="c"> <span class="p">}</span></span>
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4858
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<pre style="margin: 0;">+<span id="LC4858" class="line" lang="c"> <span class="p">}</span></span>
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4859
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<pre style="margin: 0;">+<span id="LC4859" class="line" lang="c"> </span>
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4860
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<pre style="margin: 0;">+<span id="LC4860" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">HIT</span><span class="p">)</span> <span class="p">{</span></span>
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4861
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<pre style="margin: 0;">+<span id="LC4861" class="line" lang="c"> <span class="n" style="color: #333;">V_score</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">V_scores</span><span class="p">;</span></span>
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4862
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<pre style="margin: 0;">+<span id="LC4862" class="line" lang="c"> <span class="n" style="color: #333;">V_score</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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4863
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<pre style="margin: 0;">+<span id="LC4863" class="line" lang="c"> <span class="n" style="color: #333;">V_score</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="p">(</span><span class="n" style="color: #333;">last</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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4864
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<pre style="margin: 0;">+<span id="LC4864" class="line" lang="c"> <span class="n" style="color: #333;">V_score</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">next</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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4865
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<pre style="margin: 0;">+<span id="LC4865" class="line" lang="c"> <span class="n" style="color: #333;">Ms</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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4866
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<pre style="margin: 0;">+<span id="LC4866" class="line" lang="c"> <span class="n" style="color: #333;">MMs</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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4867
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<pre style="margin: 0;">+<span id="LC4867" class="line" lang="c"> <span class="n" style="color: #333;">Us</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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4868
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<pre style="margin: 0;">+<span id="LC4868" class="line" lang="c"> <span class="n" style="color: #333;">W1s</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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4869
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<pre style="margin: 0;">+<span id="LC4869" class="line" lang="c"> <span class="n" style="color: #333;">gaps</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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4870
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<pre style="margin: 0;">+<span id="LC4870" 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;">1</span><span class="p">;</span> <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="p">(</span><span class="n" style="color: #333;">qseqP</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">N</span><span class="p">);</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="p">{</span></span>
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4871
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<pre style="margin: 0;">+<span id="LC4871" class="line" lang="c"> <span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">qseqP</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">N</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;">kmersize</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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4872
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<pre style="margin: 0;">+<span id="LC4872" class="line" lang="c"> <span class="k" style="font-weight: 600;">while</span><span class="p">(</span><span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">end</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4873" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4873
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<pre style="margin: 0;">+<span id="LC4873" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">((</span><span class="n" style="color: #333;">values</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">hashMap_get</span><span class="p">(</span><span class="n" style="color: #333;">templates</span><span class="p">,</span> <span class="n" style="color: #333;">getKmer</span><span class="p">(</span><span class="n" style="color: #333;">qseqP</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="n" style="color: #333;">j</span><span class="p">,</span> <span class="n" style="color: #333;">shifter</span><span class="p">))))</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4874" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4874
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<pre style="margin: 0;">+<span id="LC4874" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">values</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">last</span><span class="p">)</span> <span class="p">{</span></span>
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4875
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<pre style="margin: 0;">+<span id="LC4875" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">kmersize</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">gaps</span><span class="p">)</span> <span class="p">{</span></span>
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4876
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<pre style="margin: 0;">+<span id="LC4876" class="line" lang="c"> <span class="n" style="color: #333;">Ms</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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4877
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<pre style="margin: 0;">+<span id="LC4877" class="line" lang="c"> <span class="n" style="color: #333;">gaps</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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4878
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<pre style="margin: 0;">+<span id="LC4878" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">gaps</span><span class="p">)</span> <span class="p">{</span></span>
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4879
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<pre style="margin: 0;">+<span id="LC4879" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* go for best scenario */</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4880" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4880
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<pre style="margin: 0;">+<span id="LC4880" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">gaps</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="4881" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4881
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<pre style="margin: 0;">+<span id="LC4881" class="line" lang="c"> <span class="n" style="color: #333;">MMs</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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4882
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<pre style="margin: 0;">+<span id="LC4882" 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="4883" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4883
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<pre style="margin: 0;">+<span id="LC4883" class="line" lang="c"> <span class="n" style="color: #333;">gaps</span> <span class="o" style="font-weight: 600;">-=</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4884" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4884
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<pre style="margin: 0;">+<span id="LC4884" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">((</span><span class="n" style="color: #333;">MM</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;">gaps</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">M</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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4885
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<pre style="margin: 0;">+<span id="LC4885" class="line" lang="c"> <span class="n" style="color: #333;">Ms</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">gaps</span><span class="p">;</span></span>
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4886
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<pre style="margin: 0;">+<span id="LC4886" class="line" lang="c"> <span class="n" style="color: #333;">MMs</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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4887
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<pre style="margin: 0;">+<span id="LC4887" class="line" lang="c"> <span class="p">}</span></span>
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4888
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<pre style="margin: 0;">+<span id="LC4888" class="line" lang="c"> <span class="p">}</span></span>
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4889
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<pre style="margin: 0;">+<span id="LC4889" 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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4890
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<pre style="margin: 0;">+<span id="LC4890" class="line" lang="c"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">MMs</span><span class="p">;</span></span>
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4891
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<pre style="margin: 0;">+<span id="LC4891" class="line" lang="c"> <span class="p">}</span></span>
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4892
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<pre style="margin: 0;">+<span id="LC4892" 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;">gaps</span><span class="p">)</span> <span class="p">{</span></span>
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4893
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<pre style="margin: 0;">+<span id="LC4893" class="line" lang="c"> <span class="o" style="font-weight: 600;">--</span><span class="n" style="color: #333;">gaps</span><span class="p">;</span></span>
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4894
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<pre style="margin: 0;">+<span id="LC4894" class="line" lang="c"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">W1s</span><span class="p">;</span></span>
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4895
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<pre style="margin: 0;">+<span id="LC4895" class="line" lang="c"> <span class="n" style="color: #333;">Us</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">gaps</span><span class="p">;</span></span>
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4896
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<pre style="margin: 0;">+<span id="LC4896" 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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4897
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<pre style="margin: 0;">+<span id="LC4897" class="line" lang="c"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">Ms</span><span class="p">;</span></span>
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4898
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<pre style="margin: 0;">+<span id="LC4898" class="line" lang="c"> <span class="p">}</span></span>
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4899
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<pre style="margin: 0;">+<span id="LC4899" 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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4900
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<pre style="margin: 0;">+<span id="LC4900" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">last</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4901" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4901
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<pre style="margin: 0;">+<span id="LC4901" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* update and link between ankers */</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4902" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4902
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<pre style="margin: 0;">+<span id="LC4902" class="line" lang="c"> <span class="n" style="color: #333;">V_score</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">weight</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Ms</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">M</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">MMs</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">MM</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">Us</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">U</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">W1s</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">W1</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4903" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4903
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<pre style="margin: 0;">+<span id="LC4903" class="line" lang="c"> <span class="n" style="color: #333;">V_score</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">gaps</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="4904" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4904
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<pre style="margin: 0;">+<span id="LC4904" class="line" lang="c"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">V_score</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4905" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4905
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<pre style="margin: 0;">+<span id="LC4905" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4906" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4906
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<pre style="margin: 0;">+<span id="LC4906" class="line" lang="c"> <span class="n" style="color: #333;">V_score</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">j</span><span class="p">;</span></span>
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4907
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<pre style="margin: 0;">+<span id="LC4907" class="line" lang="c"> <span class="n" style="color: #333;">V_score</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="p">(</span><span class="n" style="color: #333;">last</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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<td class="diff-line-num new new_line" data-linenumber="4908" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4908
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<pre style="margin: 0;">+<span id="LC4908" class="line" lang="c"> <span class="n" style="color: #333;">Ms</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="4909" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4909
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<pre style="margin: 0;">+<span id="LC4909" class="line" lang="c"> <span class="n" style="color: #333;">MMs</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="4910" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4910
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<pre style="margin: 0;">+<span id="LC4910" class="line" lang="c"> <span class="n" style="color: #333;">Us</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="4911" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4911
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<pre style="margin: 0;">+<span id="LC4911" class="line" lang="c"> <span class="n" style="color: #333;">W1s</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="4912" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4912
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<pre style="margin: 0;">+<span id="LC4912" class="line" lang="c"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">hitCounter_r</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4913" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4913
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<pre style="margin: 0;">+<span id="LC4913" class="line" lang="c"> <span class="p">}</span></span>
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4914
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<pre style="margin: 0;">+<span id="LC4914" class="line" lang="c"> <span class="n" style="color: #333;">gaps</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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4915
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<pre style="margin: 0;">+<span id="LC4915" 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="4916" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4916
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<pre style="margin: 0;">+<span id="LC4916" class="line" lang="c"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">gaps</span><span class="p">;</span></span>
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4917
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<pre style="margin: 0;">+<span id="LC4917" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4918" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4918
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<pre style="margin: 0;">+<span id="LC4918" class="line" lang="c"> <span class="n" style="color: #333;">j</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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4919
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<pre style="margin: 0;">+<span id="LC4919" class="line" lang="c"> <span class="p">}</span></span>
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4920
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<pre style="margin: 0;">+<span id="LC4920" class="line" lang="c"> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">qseqP</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">N</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;">1</span><span class="p">;</span></span>
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4921
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<pre style="margin: 0;">+<span id="LC4921" class="line" lang="c"> <span class="p">}</span></span>
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4922
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<pre style="margin: 0;">+<span id="LC4922" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">last</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4923" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4923
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<pre style="margin: 0;">+<span id="LC4923" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* update anker */</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4924" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4924
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<pre style="margin: 0;">+<span id="LC4924" class="line" lang="c"> <span class="n" style="color: #333;">V_score</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">weight</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Ms</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">M</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">MMs</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">MM</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">Us</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">U</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">W1s</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">W1</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4925" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4925
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<pre style="margin: 0;">+<span id="LC4925" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4926" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4926
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<pre style="margin: 0;">+<span id="LC4926" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4927" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4927
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<pre style="margin: 0;">+<span id="LC4927" class="line" lang="c"> <span class="o" style="font-weight: 600;">--*</span><span class="p">(</span><span class="n" style="color: #333;">qseqP</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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4928
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<pre style="margin: 0;">+<span id="LC4928" class="line" lang="c"> <span class="p">}</span></span>
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4929
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<pre style="margin: 0;">+<span id="LC4929" class="line" lang="c"> </span>
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<td class="diff-line-num new new_line" data-linenumber="4930" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4930
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<pre style="margin: 0;">+<span id="LC4930" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* here */</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4931" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4931
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<pre style="margin: 0;">+<span id="LC4931" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* chaining */</span></span>
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4932
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<pre style="margin: 0;">+<span id="LC4932" class="line" lang="c"> </span>
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<td class="diff-line-num new new_line" data-linenumber="4933" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4933
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<pre style="margin: 0;">+<span id="LC4933" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/*</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4934" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4934
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<pre style="margin: 0;">+<span id="LC4934" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> while(chain is good) {</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4935" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4935
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<pre style="margin: 0;">+<span id="LC4935" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> 1. make chain. OK</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4936" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4936
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<pre style="margin: 0;">+<span id="LC4936" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> 2. choose best.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4937" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4937
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<pre style="margin: 0;">+<span id="LC4937" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> 3. silence "used" ankers.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4938" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4938
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<pre style="margin: 0;">+<span id="LC4938" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> 4. redo chaining if next best hits a silenced anker.</span></span>
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4939
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<pre style="margin: 0;">+<span id="LC4939" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> }</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4940" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4940
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<pre style="margin: 0;">+<span id="LC4940" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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4941
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<pre style="margin: 0;">+<span id="LC4941" class="line" lang="c"> </span>
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4942
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<pre style="margin: 0;">+<span id="LC4942" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/*</span></span>
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4943
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<pre style="margin: 0;">+<span id="LC4943" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> for each anker</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4944" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4944
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<pre style="margin: 0;">+<span id="LC4944" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> mark last anker w.r.t. highest score on anker</span></span>
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4945
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<pre style="margin: 0;">+<span id="LC4945" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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4946
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<pre style="margin: 0;">+<span id="LC4946" class="line" lang="c"> </span>
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4947
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<pre style="margin: 0;">+<span id="LC4947" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* make chains */</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4948" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4948
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<pre style="margin: 0;">+<span id="LC4948" class="line" lang="c"> <span class="n" style="color: #333;">maxS</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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4949
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<pre style="margin: 0;">+<span id="LC4949" class="line" lang="c"> <span class="n" style="color: #333;">V_score</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">VF_scores</span><span class="p">;</span></span>
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4950
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<pre style="margin: 0;">+<span id="LC4950" class="line" lang="c"> <span class="n" style="color: #333;">HIT</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">hitCounter</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="4951" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4951
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<pre style="margin: 0;">+<span id="LC4951" class="line" lang="c"> <span class="n" style="color: #333;">bests</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bestTemplates</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4952" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4952
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<pre style="margin: 0;">+<span id="LC4952" class="line" lang="c"> <span class="n" style="color: #333;">rc</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4953" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4953
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<pre style="margin: 0;">+<span id="LC4953" class="line" lang="c"> <span class="k" style="font-weight: 600;">while</span><span class="p">(</span><span class="n" style="color: #333;">rc</span><span class="o" style="font-weight: 600;">--</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4954" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4954
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<pre style="margin: 0;">+<span id="LC4954" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">rc</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="4955" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4955
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<pre style="margin: 0;">+<span id="LC4955" class="line" lang="c"> <span class="n" style="color: #333;">V_score</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">VR_scores</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4956" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4956
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<pre style="margin: 0;">+<span id="LC4956" class="line" lang="c"> <span class="n" style="color: #333;">HIT</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">hitCounter_r</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="4957" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4957
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<pre style="margin: 0;">+<span id="LC4957" class="line" lang="c"> <span class="n" style="color: #333;">bests</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bestTemplates_r</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4958" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4958
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<pre style="margin: 0;">+<span id="LC4958" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4959" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4959
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<pre style="margin: 0;">+<span id="LC4959" class="line" lang="c"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">bests</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="4960" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4960
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<pre style="margin: 0;">+<span id="LC4960" class="line" lang="c"> <span class="k" style="font-weight: 600;">while</span><span class="p">(</span><span class="o" style="font-weight: 600;">--</span><span class="n" style="color: #333;">HIT</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4961" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4961
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<pre style="margin: 0;">+<span id="LC4961" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/*</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4962" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4962
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<pre style="margin: 0;">+<span id="LC4962" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> Save pos of best score, and chain it (0 if local).</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4963" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4963
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<pre style="margin: 0;">+<span id="LC4963" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> Score is always current / w.r.t. the anker you are on.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4964" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4964
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<pre style="margin: 0;">+<span id="LC4964" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> extendScore contains endpos of last hit anker.</span></span>
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4965
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<pre style="margin: 0;">+<span id="LC4965" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4966" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4966
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<pre style="margin: 0;">+<span id="LC4966" class="line" lang="c"> <span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">V_score</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">start</span><span class="p">;</span></span>
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4967
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<pre style="margin: 0;">+<span id="LC4967" class="line" lang="c"> <span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">V_score</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">end</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4968" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4968
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<pre style="margin: 0;">+<span id="LC4968" class="line" lang="c"> </span>
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<td class="diff-line-num new new_line" data-linenumber="4969" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4969
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<pre style="margin: 0;">+<span id="LC4969" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* chain anker */</span></span>
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4970
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<pre style="margin: 0;">+<span id="LC4970" class="line" lang="c"> <span class="n" style="color: #333;">V_score</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4971" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4971
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<pre style="margin: 0;">+<span id="LC4971" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">SU</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4972" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4972
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<pre style="margin: 0;">+<span id="LC4972" class="line" lang="c"> <span class="n" style="color: #333;">values_s</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><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="p">)</span> <span class="n" style="color: #333;">V_score</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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<td class="diff-line-num new new_line" data-linenumber="4973" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4973
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<pre style="margin: 0;">+<span id="LC4973" 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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<td class="diff-line-num new new_line" data-linenumber="4974" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4974
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<pre style="margin: 0;">+<span id="LC4974" 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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<td class="diff-line-num new new_line" data-linenumber="4975" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4975
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<pre style="margin: 0;">+<span id="LC4975" 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="4976" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4976
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<pre style="margin: 0;">+<span id="LC4976" 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;">V_score</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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<td class="diff-line-num new new_line" data-linenumber="4977" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4977
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<pre style="margin: 0;">+<span id="LC4977" 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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<td class="diff-line-num new new_line" data-linenumber="4978" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4978
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<pre style="margin: 0;">+<span id="LC4978" 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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4979
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<pre style="margin: 0;">+<span id="LC4979" class="line" lang="c"> <span class="p">}</span></span>
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4980
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<pre style="margin: 0;">+<span id="LC4980" class="line" lang="c"> <span class="k" style="font-weight: 600;">while</span><span class="p">(</span><span class="o" style="font-weight: 600;">--</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4981" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4981
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<pre style="margin: 0;">+<span id="LC4981" class="line" lang="c"> <span class="n" style="color: #333;">template</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SU</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="o" style="font-weight: 600;">*--</span><span class="n" style="color: #333;">values</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4982" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4982
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<pre style="margin: 0;">+<span id="LC4982" 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;">include</span><span class="p">[</span><span class="n" style="color: #333;">template</span><span class="p">])</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4983" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4983
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<pre style="margin: 0;">+<span id="LC4983" class="line" lang="c"> <span class="n" style="color: #333;">include</span><span class="p">[</span><span class="n" style="color: #333;">template</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4984" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4984
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<pre style="margin: 0;">+<span id="LC4984" class="line" lang="c"> <span class="n" style="color: #333;">bests</span><span class="p">[</span><span class="o" style="font-weight: 600;">++*</span><span class="n" style="color: #333;">bests</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">template</span><span class="p">;</span></span>
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4985
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<pre style="margin: 0;">+<span id="LC4985" class="line" lang="c"> <span class="p">}</span></span>
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4986
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<pre style="margin: 0;">+<span id="LC4986" class="line" lang="c"> <span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Score</span><span class="p">[</span><span class="n" style="color: #333;">template</span><span class="p">];</span></span>
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4987
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<pre style="margin: 0;">+<span id="LC4987" class="line" lang="c"> <span class="n" style="color: #333;">gaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">-</span> <span class="p">(</span><span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">extendScore</span><span class="p">[</span><span class="n" style="color: #333;">template</span><span class="p">]);</span></span>
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4988
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<pre style="margin: 0;">+<span id="LC4988" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">gaps</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="4989" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4989
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<pre style="margin: 0;">+<span id="LC4989" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* continued match */</span></span>
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4990
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<pre style="margin: 0;">+<span id="LC4990" class="line" lang="c"> <span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">M</span><span class="p">;</span></span>
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4991
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<pre style="margin: 0;">+<span id="LC4991" 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;">gaps</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="4992" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4992
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<pre style="margin: 0;">+<span id="LC4992" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* deletion */</span></span>
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4993
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<pre style="margin: 0;">+<span id="LC4993" class="line" lang="c"> <span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">+=</span> <span class="p">(</span><span class="n" style="color: #333;">W1</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">abs</span><span class="p">(</span><span class="n" style="color: #333;">gaps</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;">U</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4994" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4994
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<pre style="margin: 0;">+<span id="LC4994" 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;">gaps</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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4995
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<pre style="margin: 0;">+<span id="LC4995" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* one unmatched between */</span></span>
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4996
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<pre style="margin: 0;">+<span id="LC4996" class="line" lang="c"> <span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">MM</span><span class="p">;</span></span>
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4997
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<pre style="margin: 0;">+<span id="LC4997" 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="4998" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4998
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<pre style="margin: 0;">+<span id="LC4998" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* unmatched bases between */</span></span>
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4999
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<pre style="margin: 0;">+<span id="LC4999" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">((</span><span class="n" style="color: #333;">gaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">gaps</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">2</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">M</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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5000
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<pre style="margin: 0;">+<span id="LC5000" class="line" lang="c"> <span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">gaps</span><span class="p">;</span></span>
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5001
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<pre style="margin: 0;">+<span id="LC5001" class="line" lang="c"> <span class="p">}</span></span>
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5002
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<pre style="margin: 0;">+<span id="LC5002" class="line" lang="c"> <span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">+=</span> <span class="p">(</span><span class="n" style="color: #333;">MM</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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5003
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<pre style="margin: 0;">+<span id="LC5003" class="line" lang="c"> <span class="p">}</span></span>
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5004
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<pre style="margin: 0;">+<span id="LC5004" class="line" lang="c"> </span>
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<td class="diff-line-num new new_line" data-linenumber="5005" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
5005
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<pre style="margin: 0;">+<span id="LC5005" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* check local chain is needed */</span></span>
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5006
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<pre style="margin: 0;">+<span id="LC5006" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">Wl</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="5007" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
5007
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<pre style="margin: 0;">+<span id="LC5007" class="line" lang="c"> <span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Wl</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">V_score</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">weight</span><span class="p">;</span></span>
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5008
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<pre style="margin: 0;">+<span id="LC5008" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* mark as terminating */</span></span>
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5009
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<pre style="margin: 0;">+<span id="LC5009" class="line" lang="c"> <span class="n" style="color: #333;">V_score</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">next</span> <span class="o" style="font-weight: 600;">=</span> <span class="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="5010" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
5010
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<pre style="margin: 0;">+<span id="LC5010" class="line" lang="c"> <span class="n" style="color: #333;">extendScore</span><span class="p">[</span><span class="n" style="color: #333;">template</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="5011" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
5011
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<pre style="margin: 0;">+<span id="LC5011" 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="5012" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
5012
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<pre style="margin: 0;">+<span id="LC5012" class="line" lang="c"> <span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">V_score</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">weight</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="5013" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
5013
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<pre style="margin: 0;">+<span id="LC5013" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* mark descendant */</span></span>
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<td class="diff-line-num new new_line" data-linenumber="5014" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
5014
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<pre style="margin: 0;">+<span id="LC5014" class="line" lang="c"> <span class="n" style="color: #333;">tmp_score</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">V_score</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="5015" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
5015
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<pre style="margin: 0;">+<span id="LC5015" class="line" lang="c"> <span class="k" style="font-weight: 600;">while</span><span class="p">((</span><span class="o" style="font-weight: 600;">--</span><span class="n" style="color: #333;">tmp_score</span><span class="p">)</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">pos</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="5016" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
5016
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<pre style="margin: 0;">+<span id="LC5016" class="line" lang="c"> <span class="n" style="color: #333;">V_score</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">next</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tmp_score</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="5017" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
5017
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<pre style="margin: 0;">+<span id="LC5017" class="line" lang="c"> <span class="n" style="color: #333;">extendScore</span><span class="p">[</span><span class="n" style="color: #333;">template</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">end</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="5018" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
5018
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<pre style="margin: 0;">+<span id="LC5018" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="5019" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
5019
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<pre style="margin: 0;">+<span id="LC5019" class="line" lang="c"> </span>
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<td class="diff-line-num new new_line" data-linenumber="5020" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
5020
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<pre style="margin: 0;">+<span id="LC5020" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* update Scores */</span></span>
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<td class="diff-line-num new new_line" data-linenumber="5021" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
5021
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<pre style="margin: 0;">+<span id="LC5021" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">V_score</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">score</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="5022" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
5022
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<pre style="margin: 0;">+<span id="LC5022" class="line" lang="c"> <span class="n" style="color: #333;">V_score</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">score</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="5023" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
5023
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<pre style="margin: 0;">+<span id="LC5023" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* here */</span></span>
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<td class="diff-line-num new new_line" data-linenumber="5024" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
5024
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<pre style="margin: 0;">+<span id="LC5024" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* consider several bests */</span></span>
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<td class="diff-line-num new new_line" data-linenumber="5025" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
5025
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<pre style="margin: 0;">+<span id="LC5025" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">maxS</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">score</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="5026" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
5026
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<pre style="margin: 0;">+<span id="LC5026" class="line" lang="c"> <span class="n" style="color: #333;">maxS</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">score</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="5027" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
5027
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<pre style="margin: 0;">+<span id="LC5027" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="5028" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
5028
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<pre style="margin: 0;">+<span id="LC5028" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="5029" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
5029
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<pre style="margin: 0;">+<span id="LC5029" class="line" lang="c"> <span class="n" style="color: #333;">Score</span><span class="p">[</span><span class="n" style="color: #333;">template</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">score</span><span class="p">;</span></span>
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5030
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<pre style="margin: 0;">+<span id="LC5030" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="5031" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
5031
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<pre style="margin: 0;">+<span id="LC5031" class="line" lang="c"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">V_score</span><span class="p">;</span></span>
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5032
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<pre style="margin: 0;">+<span id="LC5032" class="line" lang="c"> <span class="p">}</span></span>
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5033
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<pre style="margin: 0;">+<span id="LC5033" class="line" lang="c"> </span>
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5034
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<pre style="margin: 0;">+<span id="LC5034" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* clear Score */</span></span>
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<td class="diff-line-num new new_line" data-linenumber="5035" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
5035
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<pre style="margin: 0;">+<span id="LC5035" 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;">bests</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="5036" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
5036
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<pre style="margin: 0;">+<span id="LC5036" class="line" lang="c"> <span class="k" style="font-weight: 600;">while</span><span class="p">(</span><span class="o" style="font-weight: 600;">--</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="5037" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
5037
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<pre style="margin: 0;">+<span id="LC5037" class="line" lang="c"> <span class="n" style="color: #333;">include</span><span class="p">[</span><span class="o" style="font-weight: 600;">*++</span><span class="n" style="color: #333;">bests</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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5038
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<pre style="margin: 0;">+<span id="LC5038" class="line" lang="c"> <span class="p">}</span></span>
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5039
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<pre style="margin: 0;">+<span id="LC5039" class="line" lang="c"> <span class="n" style="color: #333;">clearScore</span><span class="p">(</span><span class="n" style="color: #333;">bests</span><span class="p">,</span> <span class="n" style="color: #333;">Score</span><span class="p">);</span></span>
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5040
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<pre style="margin: 0;">+<span id="LC5040" class="line" lang="c"> <span class="n" style="color: #333;">clearScore</span><span class="p">(</span><span class="n" style="color: #333;">bests</span><span class="p">,</span> <span class="n" style="color: #333;">extendScore</span><span class="p">);</span></span>
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5041
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<pre style="margin: 0;">+<span id="LC5041" class="line" lang="c"> <span class="p">}</span></span>
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5042
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<pre style="margin: 0;">+<span id="LC5042" class="line" lang="c"> </span>
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5043
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<pre style="margin: 0;">+<span id="LC5043" class="line" lang="c"> </span>
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5044
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<pre style="margin: 0;">+<span id="LC5044" class="line" lang="c"> </span>
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5045
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<pre style="margin: 0;">+<span id="LC5045" class="line" lang="c"> </span>
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5046
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<pre style="margin: 0;">+<span id="LC5046" class="line" lang="c"> </span>
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5047
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<pre style="margin: 0;">+<span id="LC5047" class="line" lang="c"> </span>
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5048
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<pre style="margin: 0;">+<span id="LC5048" class="line" lang="c"> </span>
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5049
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<pre style="margin: 0;">+<span id="LC5049" class="line" lang="c"> </span>
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5050
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<pre style="margin: 0;">+<span id="LC5050" class="line" lang="c"> </span>
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5051
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<pre style="margin: 0;">+<span id="LC5051" class="line" lang="c"> </span>
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5052
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<pre style="margin: 0;">+<span id="LC5052" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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5053
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<pre style="margin: 0;">+<span id="LC5053" class="line" lang="c"><span class="p">}</span></span></pre>
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<a href="https://salsa.debian.org/med-team/kma/commit/f5137c3d39949889292033da254f861b4981ebbf#5e9149468b1d12c9eb149b26487ea1dfd176a6de"><strong>savekmers.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">@@ -25,6 +25,8 @@</td>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifndef SAVEKMERS</span></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="c"><span class="k" style="font-weight: 600;">typedef</span> <span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">kmerScan_thread</span> <span class="n" style="color: #333;">KmerScan_thread</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="c"><span class="k" style="font-weight: 600;">typedef</span> <span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">kmerAnker</span> <span class="n" style="color: #333;">KmerAnker</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="c"><span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">kmerScan_thread</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;">pthread_t</span> <span class="n" style="color: #333;">id</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;">num</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">@@ -40,6 +42,16 @@ struct kmerScan_thread {</td>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="c"> <span class="n" style="color: #333;">Penalties</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">rewards</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="c"> <span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">kmerScan_thread</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">next</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="c"><span class="p">};</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="c"><span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">kmerAnker</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">score</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">weight</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">start</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">end</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC51" 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>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="c"> <span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">kmerAnker</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">next</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="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>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define SAVEKMERS 1;</span></span>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="c"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -84,3 +96,4 @@ int save_kmers_forcePair(const HashMapKMA *templates, const Penalties *rewards,</td>
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<pre style="margin: 0;"> <span id="LC96" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">save_kmers_HMM</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">HashMapKMA</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">templates</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Penalties</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">rewards</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">bestTemplates</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">bestTemplates_r</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">Score</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">Score_r</span><span class="p">,</span> <span class="n" style="color: #333;">CompDNA</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq</span><span class="p">,</span> <span class="n" style="color: #333;">CompDNA</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq_r</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Qseqs</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">header</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">extendScore</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">exhaustive</span><span class="p">,</span> <span class="k" style="font-weight: 600;">volatile</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">excludeOut</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">out</span><span class="p">);</span></span>
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97
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<pre style="margin: 0;"> <span id="LC97" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">ankerAndClean</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">regionTemplates</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">Score</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">Score_r</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;">include</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">template_lengths</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">VF_scores</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">VR_scores</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">tmpNs</span><span class="p">,</span> <span class="n" style="color: #333;">CompDNA</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">HIT</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">bestScore</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">start_cut</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">end_cut</span><span class="p">,</span> <span class="n" style="color: #333;">Qseqs</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">header</span><span class="p">,</span> <span class="k" style="font-weight: 600;">volatile</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">excludeOut</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">out</span><span class="p">);</span></span>
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98
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<pre style="margin: 0;"> <span id="LC98" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">ankerAndClean_MEM</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">regionTemplates</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">Score</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">Score_r</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;">include</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">template_lengths</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">VF_scores</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">VR_scores</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">tmpNs</span><span class="p">,</span> <span class="n" style="color: #333;">CompDNA</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">HIT</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">bestScore</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">start_cut</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">end_cut</span><span class="p">,</span> <span class="n" style="color: #333;">Qseqs</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">header</span><span class="p">,</span> <span class="k" style="font-weight: 600;">volatile</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">excludeOut</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">out</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">save_kmers_chain</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">HashMapKMA</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">templates</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Penalties</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">rewards</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">bestTemplates</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">bestTemplates_r</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">Score</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">Score_r</span><span class="p">,</span> <span class="n" style="color: #333;">CompDNA</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq</span><span class="p">,</span> <span class="n" style="color: #333;">CompDNA</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qseq_r</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Qseqs</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">header</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">extendScore</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">exhaustive</span><span class="p">,</span> <span class="k" style="font-weight: 600;">volatile</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">excludeOut</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">out</span><span class="p">);</span></span></pre>
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<a href="https://salsa.debian.org/med-team/kma/commit/f5137c3d39949889292033da254f861b4981ebbf#7fa02bd1b412f83275abb82df0572b57f1958a70"><strong>seq2fasta.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">@@ -80,8 +80,7 @@ void printFastas(char *filename, int *template_lengths) {</td>
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<pre style="margin: 0;"> <span id="LC80" 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;">seq</span> <span class="o" style="font-weight: 600;">||</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">compseq</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="c"> <span class="n" style="color: #333;">ERROR</span><span class="p">();</span></span>
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC83" class="line" lang="c"> </span>
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<pre style="margin: 0;">-<span id="LC84" 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;">1</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">DB_size</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC83" 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;">1</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">DB_size</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="p">{</span></span>
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85
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84
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="c"> <span class="n" style="color: #333;">fread</span><span class="p">(</span><span class="n" style="color: #333;">compseq</span><span class="p">,</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span><span class="p">),</span> <span class="p">(</span><span class="n" style="color: #333;">template_lengths</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;">5</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">seqfile</span><span class="p">);</span></span>
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86
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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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87
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86
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="c"> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">template_lengths</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="103" style="width: 35px; color: rgba(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="102" style="width: 35px; color: rgba(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">@@ -103,7 +102,7 @@ void printFastaList(char *filename, int *template_lengths, int *seqlist) {</td>
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103
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102
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<pre style="margin: 0;"> <span id="LC102" class="line" lang="c"> </span>
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104
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103
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<pre style="margin: 0;"> <span id="LC103" 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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<td class="diff-line-num old_line" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
105
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104
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<pre style="margin: 0;"> <span id="LC104" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">j</span><span class="p">,</span> <span class="n" style="color: #333;">n</span><span class="p">,</span> <span class="n" style="color: #333;">max</span><span class="p">,</span> <span class="n" style="color: #333;">DB_size</span><span class="p">,</span> <span class="n" style="color: #333;">file_len</span><span class="p">;</span></span>
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106
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<pre style="margin: 0;">-<span id="LC106" class="line" lang="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;">compseq</span><span class="p">;</span></span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="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;"><span class="idiff left">skip</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">compseq</span><span class="p">;</span></span>
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107
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106
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<pre style="margin: 0;"> <span id="LC106" 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;">seq</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
108
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107
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<pre style="margin: 0;"> <span id="LC107" 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;">seqfile</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">namefile</span><span class="p">;</span></span>
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109
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108
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<pre style="margin: 0;"> <span id="LC108" class="line" lang="c"> <span class="n" style="color: #333;">Qseqs</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">template_name</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="139" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="138" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -139,11 +138,13 @@ void printFastaList(char *filename, int *template_lengths, int *seqlist) {</td>
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139
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138
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<pre style="margin: 0;"> <span id="LC138" 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;">seq</span> <span class="o" style="font-weight: 600;">||</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">compseq</span><span class="p">)</span> <span class="p">{</span></span>
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140
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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;">ERROR</span><span class="p">();</span></span>
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141
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140
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<pre style="margin: 0;"> <span id="LC140" class="line" lang="c"> <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>
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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;">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;">1</span><span class="p">;</span> <span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">DB_size</span><span class="p">;</span> <span class="n" style="color: #333;"><span class="idiff left">i</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">++</span></span><span class="p">)</span> <span class="p">{</span></span>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="c"> <span class="n" style="color: #333;"><span class="idiff left">skip</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff right">;</span></span></span>
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142
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<pre style="margin: 0;">+<span id="LC142" 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;">1</span><span class="p">;</span> <span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">DB_size</span><span class="p">;</span> <span class="o" style="font-weight: 600;"><span class="idiff left">++</span></span><span class="n" style="color: #333;"><span class="idiff right">i</span></span><span class="p">)</span> <span class="p">{</span></span>
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144
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<td class="diff-line-num new_line" data-linenumber="143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
143
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<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;">i</span> <span class="o" style="font-weight: 600;">==</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">seqlist</span><span class="p">)</span> <span class="p">{</span></span>
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145
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144
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<pre style="margin: 0;"> <span id="LC144" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* get seq */</span></span>
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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;">fseek</span><span class="p">(</span><span class="n" style="color: #333;">seqfile</span><span class="p">,</span> <span class="n" style="color: #333;">skip</span><span class="p">,</span> <span class="n" style="color: #333;">SEEK_CUR</span><span class="p">);</span></span>
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146
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146
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<pre style="margin: 0;"> <span id="LC146" class="line" lang="c"> <span class="n" style="color: #333;">fread</span><span class="p">(</span><span class="n" style="color: #333;">compseq</span><span class="p">,</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span><span class="p">),</span> <span class="p">(</span><span class="n" style="color: #333;">template_lengths</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;">5</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">seqfile</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="147" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="c"> </span>
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147
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<td class="diff-line-num new_line" data-linenumber="148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
148
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<pre style="margin: 0;"> <span id="LC148" class="line" lang="c"> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">template_lengths</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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148
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<td class="diff-line-num new_line" data-linenumber="149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
149
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<pre style="margin: 0;"> <span id="LC149" class="line" lang="c"> <span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">j</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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149
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150
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<pre style="margin: 0;"> <span id="LC150" class="line" lang="c"> <span class="k" style="font-weight: 600;">while</span><span class="p">(</span><span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">--</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="156" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -156,8 +157,10 @@ void printFastaList(char *filename, int *template_lengths, int *seqlist) {</td>
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156
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157
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<pre style="margin: 0;"> <span id="LC157" class="line" lang="c"> </span>
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157
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<td class="diff-line-num new_line" data-linenumber="158" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
158
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<pre style="margin: 0;"> <span id="LC158" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* get next target */</span></span>
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158
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<td class="diff-line-num new_line" data-linenumber="159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
159
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<pre style="margin: 0;"> <span id="LC159" class="line" lang="c"> <span class="k" style="font-weight: 600;">while</span><span class="p">(</span><span class="o" style="font-weight: 600;">--</span><span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">==</span> <span class="o" style="font-weight: 600;">*++</span><span class="n" style="color: #333;">seqlist</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="c"> <span class="n" style="color: #333;">skip</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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159
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161
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<pre style="margin: 0;"> <span id="LC161" 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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160
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<td class="diff-line-num new_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">
162
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<pre style="margin: 0;"> <span id="LC162" class="line" lang="c"> <span class="n" style="color: #333;">nameSkip</span><span class="p">(</span><span class="n" style="color: #333;">namefile</span><span class="p">,</span> <span class="n" style="color: #333;">max</span><span class="p">);</span></span>
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163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="c"> <span class="n" style="color: #333;">skip</span> <span class="o" style="font-weight: 600;">+=</span> <span class="p">(((</span><span class="n" style="color: #333;">template_lengths</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;">5</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span><span class="p">));</span></span>
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161
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164
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<pre style="margin: 0;"> <span id="LC164" class="line" lang="c"> <span class="p">}</span></span>
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162
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165
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<pre style="margin: 0;"> <span id="LC165" class="line" lang="c"> <span class="p">}</span></span>
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163
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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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<a href="https://salsa.debian.org/med-team/kma/commit/f5137c3d39949889292033da254f861b4981ebbf#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">@@ -42,6 +42,7 @@</td>
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42
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "spltdb.h"</span></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "stdnuc.h"</span></span>
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<pre style="margin: 0;"> <span id="LC44" 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="LC45" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "tmp.h"</span></span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "updatescores.h"</span></span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "version.h"</span></span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "vcf.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">@@ -522,7 +523,7 @@ int runKMA_spltDB(char **templatefilenames, int targetNum, char *outputfilename,</td>
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<pre style="margin: 0;"> <span id="LC523" 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="LC524" 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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<pre style="margin: 0;"> <span id="LC525" class="line" lang="c"> <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;">frag_out_raw</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tmp<span class="idiff left">file</span></span><span class="p"><span class="idiff right">(</span>);</span></span>
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<pre style="margin: 0;">+<span id="LC526" class="line" lang="c"> <span class="n" style="color: #333;">frag_out_raw</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tmp<span class="idiff left">F</span></span><span class="p"><span class="idiff">(</span></span><span class="mi" style="color: #099;"><span class="idiff right">0</span></span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC527" 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;">frag_out_raw</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC528" class="line" lang="c"> <span class="n" style="color: #333;">ERROR</span><span class="p">();</span></span>
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<pre style="margin: 0;"> <span id="LC529" class="line" lang="c"> <span class="p">}</span></span>
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<a href="https://salsa.debian.org/med-team/kma/commit/f5137c3d39949889292033da254f861b4981ebbf#1c6375d34d9e418d1139bd146337fb256ac24a2a"><strong>tmp.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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<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 class="cp" style="color: #999; font-weight: 600;">#define _XOPEN_SOURCE 600</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <stdlib.h></span></span>
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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 <stdio.h></span></span>
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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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<pre style="margin: 0;">+<span id="LC24" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "pherror.h"</span></span>
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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 "threader.h"</span></span>
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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 "tmp.h"</span></span>
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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="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span> <span class="nf" style="color: #900; font-weight: 600;">tmpF</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">location</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="c"> </span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="c"> <span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">tmpNum</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="LC31" class="line" lang="c"> <span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">tmpname</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">dirname</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">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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<pre style="margin: 0;">+<span id="LC32" class="line" lang="c"> <span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">volatile</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">lock</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="mi" style="color: #099;">0</span><span class="p">};</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">fd</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;">FILE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">file</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="c"> </span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="c"> <span class="n" style="color: #333;">lock</span><span class="p">(</span><span class="n" style="color: #333;">lock</span><span class="p">);</span></span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">location</span><span class="p">)</span> <span class="p">{</span></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;">/* set location for tmpfiles */</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;">filename</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="n" style="color: #333;">free</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="LC41" 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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<pre style="margin: 0;">+<span id="LC42" 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;">dirname</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="c"> <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">dirname</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="c"> <span class="n" style="color: #333;">dirname</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="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="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;">location</span><span class="p">)</span> <span class="p">{</span></span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">location</span><span class="p">[</span><span class="n" style="color: #333;">strlen</span><span class="p">(</span><span class="n" style="color: #333;">location</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="sc" style="color: #d14;">'/'</span><span class="p">)</span> <span class="p">{</span></span>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="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;">location</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">15</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;">tmpname</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">filename</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">sprintf</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="p">,</span> <span class="s" style="color: #d14;">"%s.tmp"</span><span class="p">,</span> <span class="n" style="color: #333;">location</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="c"> <span class="n" style="color: #333;">dirname</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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51
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<pre style="margin: 0;">+<span id="LC51" 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="LC52" class="line" lang="c"> <span class="n" style="color: #333;">dirname</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;">location</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">12</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="c"> <span class="n" style="color: #333;">tmpname</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dirname</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">sprintf</span><span class="p">(</span><span class="n" style="color: #333;">dirname</span><span class="p">,</span> <span class="s" style="color: #d14;">"%s.kma-"</span><span class="p">,</span> <span class="n" style="color: #333;">location</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 class="n" style="color: #333;">strcpy</span><span class="p">(</span><span class="n" style="color: #333;">tmpname</span><span class="p">,</span> <span class="s" style="color: #d14;">"XXXXXX"</span><span class="p">);</span></span>
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55
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<pre style="margin: 0;">+<span id="LC55" 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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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="c"> <span class="p">}</span></span>
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="c"> <span class="p">}</span></span>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="c"> <span class="n" style="color: #333;">file</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="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="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;">dirname</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="k" style="font-weight: 600;">if</span><span class="p">((</span><span class="n" style="color: #333;">fd</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mkstemp</span><span class="p">(</span><span class="n" style="color: #333;">dirname</span><span class="p">))</span> <span class="o" style="font-weight: 600;">==</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="p">{</span></span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="c"> <span class="n" style="color: #333;">ERROR</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="k" style="font-weight: 600;">if</span><span class="p">((</span><span class="n" style="color: #333;">file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fdopen</span><span class="p">(</span><span class="n" style="color: #333;">fd</span><span class="p">,</span> <span class="s" style="color: #d14;">"wb+"</span><span class="p">)))</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;">unlink</span><span class="p">(</span><span class="n" style="color: #333;">dirname</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 class="p">}</span></span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="c"> <span class="n" style="color: #333;">strcpy</span><span class="p">(</span><span class="n" style="color: #333;">tmpname</span><span class="p">,</span> <span class="s" style="color: #d14;">"XXXXXX"</span><span class="p">);</span></span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="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;">filename</span><span class="p">)</span> <span class="p">{</span></span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* open tmpfile on previous location */</span></span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="c"> <span class="n" style="color: #333;">sprintf</span><span class="p">(</span><span class="n" style="color: #333;">tmpname</span><span class="p">,</span> <span class="s" style="color: #d14;">"%d"</span><span class="p">,</span> <span class="n" style="color: #333;">tmpNum</span><span class="o" style="font-weight: 600;">++</span><span class="p">);</span></span>
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70
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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;">file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fopen</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="p">,</span> <span class="s" style="color: #d14;">"wb+"</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;">unlink</span><span class="p">(</span><span class="n" style="color: #333;">filename</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="p">}</span></span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="c"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">tmpname</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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74
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<pre style="margin: 0;">+<span id="LC74" 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="LC75" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* open a "normal" tmp file */</span></span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="c"> <span class="n" style="color: #333;">file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tmpfile</span><span class="p">();</span></span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="c"> <span class="n" style="color: #333;">unlock</span><span class="p">(</span><span class="n" style="color: #333;">lock</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="c"> </span>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">file</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="c"><span class="p">}</span></span>
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<li id="b09c88ef20c9c024eb7272d240bf1ef251d38efa">
<a href="https://salsa.debian.org/med-team/kma/commit/f5137c3d39949889292033da254f861b4981ebbf#b09c88ef20c9c024eb7272d240bf1ef251d38efa"><strong>tmp.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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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * All rights reserved.</span></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * </span></span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * 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="cp" style="color: #999; font-weight: 600;">#include <stdio.h></span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC22" 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="nf" style="color: #900; font-weight: 600;">tmpF</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">location</span><span class="p">);</span></span></pre>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -17,4 +17,4 @@</td>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * limitations under the License.</span></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">*/</span></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define KMA_VERSION "1.2.<span class="idiff left right">6</span>"</span></span></pre>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define KMA_VERSION "1.2.<span class="idiff left right">10a</span>"</span></span></pre>
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