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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/miniasm">Debian Med / miniasm</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/miniasm/commit/89afb8f0553ede196343160c8cc7ec3fc2c971f0">89afb8f0</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-07-24T06:51:39+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 0.3+dfsg</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/miniasm/commit/d3005085ef8788a233e5ea776747ef5bfd48d680">d3005085</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-07-24T06:51:39+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/0.3+dfsg'
Update to upstream version '0.3+dfsg'
with Debian dir ab22263aaae78edd3503ea4153ecddcad210d45e</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/miniasm/commit/70eba5a57537b360cecda41f3df1d71d0a22cd1e">70eba5a5</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-07-24T06:55:51+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/miniasm/commit/d7b6c4f3557ddd7602088589e02ff4ef9e874444">d7b6c4f3</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-07-24T06:57:48+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to unstable
</pre>
</li>
</ul>
<h4>19 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#836efb6e25a091dcb4ff8e1dbb2f0be6a5cbf14c">
Makefile
</a>
</li>
<li class="file-stats">
<a href="#af7229e66d31ea23607af83900bb179046a91bf5">
PAF.md
</a>
</li>
<li class="file-stats">
<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
README.md
</a>
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<li class="file-stats">
<a href="#4ac065c3911e996984de0a7878846116cf1be057">
asm.c
</a>
</li>
<li class="file-stats">
<a href="#e25f9d52b876786bfa1c7fd2b1f1e9ce63820bf0">
common.c
</a>
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<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
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<li class="file-stats">
<a href="#d6c09299b1f914372840e8fd6fcc850f8a11b236">
debian/patches/hardening
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<li class="file-stats">
<a href="#e4c19aed51618bf0c7ebd03189c67e422f84d4eb">
debian/patches/spelling
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<li class="file-stats">
<a href="#a06db644591a8b2b7560cd2366cfe2843bfb055d">
dotter.c
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</li>
<li class="file-stats">
<a href="#9d47da796a93d0d635807cf48d76cfb19468f1e0">
hit.c
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</li>
<li class="file-stats">
<a href="#406e031b8824ea26ae0bf4d7579a1d89e3fb5906">
main.c
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<li class="file-stats">
<a href="#bb2117c4db3ac04cd9d344fb347a1ff30181fa06">
miniasm.1
</a>
</li>
<li class="file-stats">
<a href="#6091887a096fc27c98e524e1c34ccdb367c5703d">
miniasm.h
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</li>
<li class="file-stats">
<a href="#147dae8884008957fecbb07b1b51ec7cb51a9644">
misc/da2paf.pl
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</li>
<li class="file-stats">
<a href="#22b27b676f55c1a3e373e08746bba43d6414a001">
misc/mhap2paf.pl
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<li class="file-stats">
<a href="#1942408037af3fd9372960c502323746c412a36d">
<span class="new-file">
+
misc/ov-sen.js
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<li class="file-stats">
<a href="#900271b74f3c1bc24ab7b5dae82089fe297cedde">
<span class="new-file">
+
misc/paftop.js
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<li class="file-stats">
<a href="#54c16df25fed2df36be836f971ed39d117781c0d">
misc/sam2paf.js
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<li class="file-stats">
<a href="#e311dec91606c22084cc17eb781191d38d7cd6c2">
<span class="new-file">
+
misc/wt2paf.pl
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</li>
</ul>
<h4>Changes:</h4>
<li id="836efb6e25a091dcb4ff8e1dbb2f0be6a5cbf14c">
<a href="https://salsa.debian.org/med-team/miniasm/compare/c23b2121ec3f8082bbb02499edea827181a76fda...d7b6c4f3557ddd7602088589e02ff4ef9e874444#836efb6e25a091dcb4ff8e1dbb2f0be6a5cbf14c"><strong>Makefile</strong></a>
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1
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1" class="line" lang="make"><span class="nv" style="color: teal;">CC</span><span class="o" style="font-weight: 600;">=</span> gcc</span>
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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC2" class="line" lang="make"><span class="nv" style="color: teal;">CFLAGS</span><span class="o" style="font-weight: 600;">=</span> <span class="nt" style="color: navy;">-g</span> <span class="nt" style="color: navy;">-Wall</span> <span class="nt" style="color: navy;">-O2</span> <span class="nt" style="color: navy;">-Wc</span>++-compat<span class="idiff left"> </span><span class="nt" style="color: navy;"><span class="idiff right">-Wno-unused-function</span></span></span>
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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: teal;">CFLAGS</span><span class="o" style="font-weight: 600;">=</span> <span class="nt" style="color: navy;">-g</span> <span class="nt" style="color: navy;">-Wall</span> <span class="nt" style="color: navy;">-O2</span> <span class="nt" style="color: navy;">-Wc</span>++-compat</span>
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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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<pre style="margin: 0;"> <span id="LC3" class="line" lang="make"><span class="nv" style="color: teal;">CPPFLAGS</span><span class="o" style="font-weight: 600;">=</span></span>
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<td class="diff-line-num old_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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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC4" class="line" lang="make"><span class="nv" style="color: teal;">INCLUDES</span><span class="o" style="font-weight: 600;">=</span> <span class="nt" style="color: navy;">-I</span>.</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="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC5" class="line" lang="make"><span class="nv" style="color: teal;">OBJS</span><span class="o" style="font-weight: 600;">=</span> sys.o sdict.o paf.o asg.o common.o hit.o asm.o</span>
</pre>
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<li id="af7229e66d31ea23607af83900bb179046a91bf5">
<a href="https://salsa.debian.org/med-team/miniasm/compare/c23b2121ec3f8082bbb02499edea827181a76fda...d7b6c4f3557ddd7602088589e02ff4ef9e874444#af7229e66d31ea23607af83900bb179046a91bf5"><strong>PAF.md</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="22" style="width: 35px; color: rgba(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="22" style="width: 35px; color: rgba(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">@@ -22,7 +22,7 @@ following predefined fields:</td>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="markdown">If PAF is generated from an alignment, column 10 equals the number of sequence</span>
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<td class="diff-line-num old_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="markdown">matches, and column 11 equals the total number of sequence matches, mismatches,</span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="markdown">insertions and deletions in the alignment. If alignment is not available,</span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="markdown">column 10 and 11 are still required but <span class="idiff left right">can be approxim</span>ate.</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="markdown">column 10 and 11 are still required but <span class="idiff left right">may be highly inaccur</span>ate.</span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="markdown">A PAF file may optionally contain SAM-like typed key-value pairs at the end of</span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="markdown">each line.</span></pre>
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<li id="8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
<a href="https://salsa.debian.org/med-team/miniasm/compare/c23b2121ec3f8082bbb02499edea827181a76fda...d7b6c4f3557ddd7602088589e02ff4ef9e874444#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d"><strong>README.md</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="markdown"><span class="ge" style="font-style: italic;">*Warning: since r104, miniasm only works with minimap-r122 or later*</span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Getting Started</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="markdown"><span class="p">```</span><span class="nl">sh</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -7,10 +5,10 @@</td>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="markdown">wget <span class="nt" style="color: navy;">-O-</span> http://www.cbcb.umd.edu/software/PBcR/data/selfSampleData.tar.gz | <span class="nb" style="color: #0086b3;">tar </span>zxf -</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="markdown"><span class="nb" style="color: #0086b3;">ln</span> <span class="nt" style="color: navy;">-s</span> selfSampleData/pacbio_filtered.fastq reads.fq</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="markdown"><span class="c" style="color: #998; font-style: italic;"># Install minimap and miniasm (requiring gcc and zlib)</span></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="markdown">git clone https://github.com/lh3/minimap<span class="idiff left"> </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="nb" style="color: #0086b3;"><span class="idiff">cd </span></span><span class="idiff right">minimap</span> <span class="o" style="font-weight: 600;">&&</span> make<span class="o" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="markdown">git clone https://github.com/lh3/miniasm <span class="o" style="font-weight: 600;"><span class="idiff left">&&</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">(</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">cd </span></span><span class="idiff right">miniasm</span> <span class="o" style="font-weight: 600;">&&</span> make<span class="o" style="font-weight: 600;">)</span></span>
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12
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="markdown"><span class="c" style="color: #998; font-style: italic;"># Overlap</span></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="markdown">minimap<span class="idiff left">/minimap </span><span class="nt" style="color: navy;"><span class="idiff">-Sw5</span></span><span class="idiff"> </span><span class="nt" style="color: navy;"><span class="idiff">-L100</span></span><span class="idiff"> </span><span class="nt" style="color: navy;"><span class="idiff">-m0</span></span><span class="idiff"> </span><span class="nt" style="color: navy;"><span class="idiff">-t8</span></span><span class="idiff right"> reads.fq </span>reads.fq | <span class="nb" style="color: #0086b3;">gzip</span> <span class="nt" style="color: navy;">-1</span> <span class="o" style="font-weight: 600;">></span> reads.paf.gz</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="markdown">git clone https://github.com/lh3/minimap<span class="idiff left">2 </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="nb" style="color: #0086b3;"><span class="idiff">cd </span></span><span class="idiff right">minimap2</span> <span class="o" style="font-weight: 600;">&&</span> make<span class="o" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="markdown">git clone https://github.com/lh3/miniasm <span class="idiff left"> </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="nb" style="color: #0086b3;"><span class="idiff">cd </span></span><span class="idiff right">miniasm </span> <span class="o" style="font-weight: 600;">&&</span> make<span class="o" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="markdown"><span class="c" style="color: #998; font-style: italic;"># Overlap<span class="idiff left right"> for PacBio reads (or use "-x map-ont" for nanopore read overlapping)</span></span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="markdown">minimap<span class="idiff left">2/minimap2 </span><span class="nt" style="color: navy;"><span class="idiff">-x</span></span><span class="idiff"> map-pb </span><span class="nt" style="color: navy;"><span class="idiff">-t8</span></span><span class="idiff right"> pb-reads.fq pb-</span>reads.fq | <span class="nb" style="color: #0086b3;">gzip</span> <span class="nt" style="color: navy;">-1</span> <span class="o" style="font-weight: 600;">></span> reads.paf.gz</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="markdown"><span class="c" style="color: #998; font-style: italic;"># Layout</span></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="markdown">miniasm/miniasm <span class="nt" style="color: navy;">-f</span> reads.fq reads.paf.gz <span class="o" style="font-weight: 600;">></span> reads.gfa</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="markdown"><span class="p">```</span></span>
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<li id="4ac065c3911e996984de0a7878846116cf1be057">
<a href="https://salsa.debian.org/med-team/miniasm/compare/c23b2121ec3f8082bbb02499edea827181a76fda...d7b6c4f3557ddd7602088589e02ff4ef9e874444#4ac065c3911e996984de0a7878846116cf1be057"><strong>asm.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">@@ -45,10 +45,10 @@ void ma_sg_print(const asg_t *g, const sdict_t *d, const ma_sub_t *sub, FILE *fp</td>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">asg_arc_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">p</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">g</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">arc</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">sub</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">ma_sub_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">sq</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">sub</span><span class="p">[</span><span class="n" style="color: #333;">p</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">ul</span><span class="o" style="font-weight: 600;">>></span><span class="mi" style="color: #099;">33</span><span class="p">],</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">st</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">sub</span><span class="p">[</span><span class="n" style="color: #333;">p</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">v</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="LC48" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">,</span> <span class="s" style="color: #d14;">"L</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%s:%d-%d</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%c</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%s:%d-%d</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%c</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%d<span class="idiff left">M</span></span><span class="se" style="color: #d14;"><span class="idiff">\t</span></span><span class="s" style="color: #d14;"><span class="idiff right">SD</span>:i:%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;">d</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;">p</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">ul</span><span class="o" style="font-weight: 600;">>></span><span class="mi" style="color: #099;">33</span><span class="p">].</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">sq</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">sq</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">e</span><span class="p">,</span> <span class="s" style="color: #d14;">"+-"</span><span class="p">[</span><span class="n" style="color: #333;">p</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">ul</span><span class="o" style="font-weight: 600;">>></span><span class="mi" style="color: #099;">32</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="LC48" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">,</span> <span class="s" style="color: #d14;">"L</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%s:%d-%d</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%c</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%s:%d-%d</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%c</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%d<span class="idiff left">:</span></span><span class="se" style="color: #d14;"><span class="idiff">\t</span></span><span class="s" style="color: #d14;"><span class="idiff right">L1</span>:i:%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;">d</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;">p</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">ul</span><span class="o" style="font-weight: 600;">>></span><span class="mi" style="color: #099;">33</span><span class="p">].</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">sq</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">sq</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">e</span><span class="p">,</span> <span class="s" style="color: #d14;">"+-"</span><span class="p">[</span><span class="n" style="color: #333;">p</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">ul</span><span class="o" style="font-weight: 600;">>></span><span class="mi" style="color: #099;">32</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="LC49" 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;">seq</span><span class="p">[</span><span class="n" style="color: #333;">p</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">v</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;">name</span><span class="p">,</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">st</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">e</span><span class="p">,</span> <span class="s" style="color: #d14;">"+-"</span><span class="p">[</span><span class="n" style="color: #333;">p</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">v</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;">p</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">ol</span><span class="p">,</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="p">)</span><span class="n" style="color: #333;">p</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">ul</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC50" 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="LC51" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">,</span> <span class="s" style="color: #d14;">"L</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%c</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%c</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%d<span class="idiff left">M</span></span><span class="se" style="color: #d14;"><span class="idiff">\t</span></span><span class="s" style="color: #d14;"><span class="idiff right">SD</span>:i:%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;">d</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;">p</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">ul</span><span class="o" style="font-weight: 600;">>></span><span class="mi" style="color: #099;">33</span><span class="p">].</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="s" style="color: #d14;">"+-"</span><span class="p">[</span><span class="n" style="color: #333;">p</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">ul</span><span class="o" style="font-weight: 600;">>></span><span class="mi" style="color: #099;">32</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="LC51" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">,</span> <span class="s" style="color: #d14;">"L</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%c</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%s</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%c</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%d<span class="idiff left">:</span></span><span class="se" style="color: #d14;"><span class="idiff">\t</span></span><span class="s" style="color: #d14;"><span class="idiff right">L1</span>:i:%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;">d</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;">p</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">ul</span><span class="o" style="font-weight: 600;">>></span><span class="mi" style="color: #099;">33</span><span class="p">].</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="s" style="color: #d14;">"+-"</span><span class="p">[</span><span class="n" style="color: #333;">p</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">ul</span><span class="o" style="font-weight: 600;">>></span><span class="mi" style="color: #099;">32</span><span class="o" style="font-weight: 600;">&</span><span class="mi" style="color: #099;">1</span><span class="p">],</span></span>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="c"> <span class="n" style="color: #333;">d</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;">p</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">v</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;">name</span><span class="p">,</span> <span class="s" style="color: #d14;">"+-"</span><span class="p">[</span><span class="n" style="color: #333;">p</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">v</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;">p</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">ol</span><span class="p">,</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="p">)</span><span class="n" style="color: #333;">p</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">ul</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 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">@@ -8,7 +8,6 @@ void ma_opt_init(ma_opt_t *opt)</td>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="c"> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">min_match</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">100</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="c"> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">min_dp</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="LC10" class="line" lang="c"> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">min_iden</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">.</span><span class="mo" style="color: #099;">05</span><span class="p">;</span></span>
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11
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="c"> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">cov_ratio</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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12
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11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="c"> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">max_hang</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1000</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="c"> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">min_ovlp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">min_span</span><span class="p">;</span></span>
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<a href="https://salsa.debian.org/med-team/miniasm/compare/c23b2121ec3f8082bbb02499edea827181a76fda...d7b6c4f3557ddd7602088589e02ff4ef9e874444#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">miniasm (0.<span class="idiff left right">2+dfsg-4) UNRELEASED</span>; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">miniasm (0.<span class="idiff left right">3+dfsg-1) unstable</span>; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext"> * Stumbled upon code copy of some git commit in third party software</span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext"> (Unicycler) and asked for clarification about releases in</span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext"> https://github.com/lh3/miniasm/issues/51</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * Team upload</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * New upstream version</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Tue, <span class="idiff left right">17 Jul 2018 08:42:58</span> +0200</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Tue, <span class="idiff left right">24 Jul 2018 06:56:06</span> +0200</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">miniasm (0.2+dfsg-3) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"></span>
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<a href="https://salsa.debian.org/med-team/miniasm/compare/c23b2121ec3f8082bbb02499edea827181a76fda...d7b6c4f3557ddd7602088589e02ff4ef9e874444#d6c09299b1f914372840e8fd6fcc850f8a11b236"><strong>debian/patches/hardening</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -5,13 +5,13 @@ Last-Update: 2016-01-14</td>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/Makefile</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1,6 +1,5 @@</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="diff"> CC= gcc</span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-CFLAGS= -g -Wall -O2 -Wc++-compat<span class="idiff left right"> -Wno-unused-function</span></span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-CFLAGS= -g -Wall -O2 -Wc++-compat</span></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-CPPFLAGS=</span></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+CFLAGS+= -g -Wall -O2 -Wc++-compat<span class="idiff left right"> -Wno-unused-function</span></span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+CFLAGS+= -g -Wall -O2 -Wc++-compat</span></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="diff"> INCLUDES= -I.</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="diff"> OBJS= sys.o sdict.o paf.o asg.o common.o hit.o asm.o</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="diff"> PROG= miniasm minidot</span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -9,15 +8,15 @@</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -9,15 +8,15 @@<span class="idiff left right"> LIBS= -lm -lz -lpthread</span></span></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="diff"> .SUFFIXES:.c .o</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="diff"> .c.o:</span>
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<li id="e4c19aed51618bf0c7ebd03189c67e422f84d4eb">
<a href="https://salsa.debian.org/med-team/miniasm/compare/c23b2121ec3f8082bbb02499edea827181a76fda...d7b6c4f3557ddd7602088589e02ff4ef9e874444#e4c19aed51618bf0c7ebd03189c67e422f84d4eb"><strong>debian/patches/spelling</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">@@ -2,7 +2,7 @@ Description: spelling</td>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="diff">Author: Sascha Steinbiss <satta@debian.org></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/miniasm.1</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/miniasm.1</span></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1<span class="idiff left right">38,7 +138,7 @@</span></span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1<span class="idiff left right">53,7 +153,7 @@ sequences.</span></span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff"> Max and min overlap drop ratio [0.7,0.5]. Let overlap(v->w) be the overlap</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="diff"> length of edge v->w and maxovlp(v)=max_w{overlap(v->w)} be the length of</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="diff"> largest overlap. Miniasm drops overlap v->w if overlap(v->w)/maxovlp(v) is below</span>
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<a href="https://salsa.debian.org/med-team/miniasm/compare/c23b2121ec3f8082bbb02499edea827181a76fda...d7b6c4f3557ddd7602088589e02ff4ef9e874444#a06db644591a8b2b7560cd2366cfe2843bfb055d"><strong>dotter.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">@@ -91,19 +91,23 @@ int main(int argc, char *argv[])</td>
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="c"> <span class="n" style="color: #333;">d</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sd_init</span><span class="p">();</span></span>
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC93" class="line" lang="c"> <span class="n" style="color: #333;">f</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">paf_open</span><span class="p">(</span><span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="n" style="color: #333;">optind</span><span class="p">]);</span></span>
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<pre style="margin: 0;">+<span id="LC94" 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;">f</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC95" 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;">"[E::%s] could not open PAF file %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;">__func__</span><span class="p">,</span> <span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="n" style="color: #333;">optind</span><span class="p">]);</span></span>
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<pre style="margin: 0;">+<span id="LC96" 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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<pre style="margin: 0;">+<span id="LC97" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC98" class="line" lang="c"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">paf_read</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">r</span><span class="p">)</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="c"> <span class="n" style="color: #333;">dt_hit_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">s</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">r</span><span class="p">.</span><span class="n" style="color: #333;">qe</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">r</span><span class="p">.</span><span class="n" style="color: #333;">qs</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">min_span</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">r</span><span class="p">.</span><span class="n" style="color: #333;">te</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">r</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;">min_span</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">r</span><span class="p">.</span><span class="n" style="color: #333;">ml</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">min_match</span><span class="p">)</span> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC101" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">r</span><span class="p">.</span><span class="n" style="color: #333;">ml</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">r</span><span class="p">.</span><span class="n" style="color: #333;">bl</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">min_iden</span><span class="p">)</span> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC102" class="line" lang="c"> <span class="n" style="color: #333;">kv_pushp</span><span class="p">(</span><span class="n" style="color: #333;">dt_hit_t</span><span class="p">,</span> <span class="n" style="color: #333;">h</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">s</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC99" class="line" lang="c"> <span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">qn</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sd_put</span><span class="p">(</span><span class="n" style="color: #333;">d</span><span class="p">[</span><span class="mi" style="color: #099;"><span class="idiff left right">0</span></span><span class="p">],</span> <span class="n" style="color: #333;">r</span><span class="p">.</span><span class="n" style="color: #333;">qn</span><span class="p">,</span> <span class="n" style="color: #333;">r</span><span class="p">.</span><span class="n" style="color: #333;">ql</span><span class="p">),</span> <span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">qs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">r</span><span class="p">.</span><span class="n" style="color: #333;">qs</span><span class="p">,</span> <span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">qe</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">r</span><span class="p">.</span><span class="n" style="color: #333;">qe</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC100" class="line" lang="c"> <span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">tn</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sd_put</span><span class="p">(</span><span class="n" style="color: #333;">d</span><span class="p">[</span><span class="mi" style="color: #099;"><span class="idiff left right">1</span></span><span class="p">],</span> <span class="n" style="color: #333;">r</span><span class="p">.</span><span class="n" style="color: #333;">tn</span><span class="p">,</span> <span class="n" style="color: #333;">r</span><span class="p">.</span><span class="n" style="color: #333;">tl</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="c"> <span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">qn</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sd_put</span><span class="p">(</span><span class="n" style="color: #333;">d</span><span class="p">[</span><span class="mi" style="color: #099;"><span class="idiff left right">1</span></span><span class="p">],</span> <span class="n" style="color: #333;">r</span><span class="p">.</span><span class="n" style="color: #333;">qn</span><span class="p">,</span> <span class="n" style="color: #333;">r</span><span class="p">.</span><span class="n" style="color: #333;">ql</span><span class="p">),</span> <span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">qs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">r</span><span class="p">.</span><span class="n" style="color: #333;">qs</span><span class="p">,</span> <span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">qe</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">r</span><span class="p">.</span><span class="n" style="color: #333;">qe</span><span class="p">;</span></span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="c"> <span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">tn</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sd_put</span><span class="p">(</span><span class="n" style="color: #333;">d</span><span class="p">[</span><span class="mi" style="color: #099;"><span class="idiff left right">0</span></span><span class="p">],</span> <span class="n" style="color: #333;">r</span><span class="p">.</span><span class="n" style="color: #333;">tn</span><span class="p">,</span> <span class="n" style="color: #333;">r</span><span class="p">.</span><span class="n" style="color: #333;">tl</span><span class="p">);</span></span>
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101
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105
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<pre style="margin: 0;"> <span id="LC105" class="line" lang="c"> <span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">ts</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">r</span><span class="p">.</span><span class="n" style="color: #333;">rev</span><span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">r</span><span class="p">.</span><span class="n" style="color: #333;">te</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">r</span><span class="p">.</span><span class="n" style="color: #333;">ts</span><span class="p">,</span> <span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">te</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">r</span><span class="p">.</span><span class="n" style="color: #333;">rev</span><span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">r</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;">r</span><span class="p">.</span><span class="n" style="color: #333;">te</span><span class="p">;</span></span>
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102
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106
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<pre style="margin: 0;"> <span id="LC106" class="line" lang="c"> <span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">ml</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">r</span><span class="p">.</span><span class="n" style="color: #333;">ml</span><span class="p">;</span></span>
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103
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107
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<pre style="margin: 0;"> <span id="LC107" class="line" lang="c"> <span class="p">}</span></span>
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104
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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;">paf_close</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">);</span></span>
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105
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109
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<pre style="margin: 0;"> <span id="LC109" class="line" lang="c"></span>
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106
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<pre style="margin: 0;">-<span id="LC106" 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;">2</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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110
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<pre style="margin: 0;">+<span id="LC110" 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;">2</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 class="idiff left"> </span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right">// 0 for target; 1 for query</span></span></span>
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107
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111
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<pre style="margin: 0;"> <span id="LC111" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">n</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;">i</span><span class="p">]</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">n_seq</span><span class="p">;</span></span>
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108
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112
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<pre style="margin: 0;"> <span id="LC112" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">l</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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109
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113
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<pre style="margin: 0;"> <span id="LC113" class="line" lang="c"> <span class="n" style="color: #333;">a</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">srtaux_t</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">calloc</span><span class="p">(</span><span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">srtaux_t</span><span class="p">));</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="113" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="117" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -113,22 +117,17 @@ int main(int argc, char *argv[])</td>
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113
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117
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<pre style="margin: 0;"> <span id="LC117" class="line" lang="c"> <span class="n" style="color: #333;">ks_introsort_dtx</span><span class="p">(</span><span class="n" style="color: #333;">n</span><span class="p">,</span> <span class="n" style="color: #333;">a</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]);</span></span>
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114
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118
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<pre style="margin: 0;"> <span id="LC118" 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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115
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119
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<pre style="margin: 0;"> <span id="LC119" class="line" lang="c"> <span class="n" style="color: #333;">srtaux_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">b</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">a</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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116
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<pre style="margin: 0;">-<span id="LC116" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">inv</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="117" 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">
117
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<pre style="margin: 0;">-<span id="LC117" class="line" lang="c"> <span class="n" style="color: #333;">inv</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">calloc</span><span class="p">(</span><span class="n" style="color: #333;">d</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">n_seq</span><span class="p">,</span> <span class="mi" style="color: #099;">4</span><span class="p">);</span></span>
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118
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<pre style="margin: 0;">-<span id="LC118" class="line" lang="c"> <span class="k" style="font-weight: 600;">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="n" style="color: #333;">d</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">n_seq</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>
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<pre style="margin: 0;">-<span id="LC119" class="line" lang="c"> <span class="n" style="color: #333;">inv</span><span class="p">[</span><span class="n" style="color: #333;">a</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="n" style="color: #333;">j</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;">j</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC120" 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="n" style="color: #333;">n</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>
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<pre style="margin: 0;"> <span id="LC121" class="line" lang="c"> <span class="n" style="color: #333;">b</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">].</span><span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">=</span> <span class="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;">seq</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">].</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">b</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">].</span><span class="n" style="color: #333;">tot</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">b</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">].</span><span class="n" style="color: #333;">w</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;">b</span><span class="p">[</span><span class="n" style="color: #333;">j</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;">j</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC122" 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="n" style="color: #333;">h</span><span class="p">.</span><span class="n" style="color: #333;">n</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">j</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC123" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">w</span><span class="p">,</span> <span class="n" style="color: #333;">coor</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC124" class="line" lang="c"> <span class="n" style="color: #333;">dt_hit_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">p</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">h</span><span class="p">.</span><span class="n" style="color: #333;">a</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">];</span></span>
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<pre style="margin: 0;">-<span id="LC125" class="line" lang="c"> <span class="n" style="color: #333;">srtaux_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">q</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">b</span><span class="p">[</span><span class="n" style="color: #333;">p</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;"><span class="idiff left right">t</span>n</span><span class="p">];</span></span>
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<pre style="margin: 0;">-<span id="LC126" class="line" lang="c"> <span class="n" style="color: #333;">coor</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">acclen</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="n" style="color: #333;"><span class="idiff left">inv</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">p</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">qn</span></span><span class="p"><span class="idiff">]]</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">p</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">qs</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">p</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff right">q</span>e</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>
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="c"> <span class="n" style="color: #333;">srtaux_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">q</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">b</span><span class="p">[</span><span class="n" style="color: #333;">p</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;"><span class="idiff left right">q</span>n</span><span class="p">];</span></span>
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="c"> <span class="n" style="color: #333;">coor</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">acclen</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="n" style="color: #333;"><span class="idiff left">p</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">tn</span></span><span class="p"><span class="idiff">]</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">p</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">ts</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">p</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff right">t</span>e</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>
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<pre style="margin: 0;"> <span id="LC127" class="line" lang="c"> <span class="n" style="color: #333;">w</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint64_t</span><span class="p">)(.</span><span class="mo" style="color: #099;">01</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">p</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">ml</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">p</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">ml</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">.</span><span class="mi" style="color: #099;">499</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC128" class="line" lang="c"> <span class="n" style="color: #333;">q</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">tot</span> <span class="o" style="font-weight: 600;">+=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)</span><span class="n" style="color: #333;">coor</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">w</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC129" class="line" lang="c"> <span class="n" style="color: #333;">q</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">w</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">w</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC130" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC131" class="line" lang="c"> <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">inv</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC131" 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="n" style="color: #333;">n</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="n" style="color: #333;">b</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">].</span><span class="n" style="color: #333;">tot</span> <span class="o" style="font-weight: 600;">/=</span> <span class="n" style="color: #333;">b</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">].</span><span class="n" style="color: #333;">w</span><span class="p">;</span></span>
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133
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132
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<pre style="margin: 0;"> <span id="LC132" class="line" lang="c"> <span class="n" style="color: #333;">ks_introsort_dty</span><span class="p">(</span><span class="n" style="color: #333;">n</span><span class="p">,</span> <span class="n" style="color: #333;">b</span><span class="p">);</span></span>
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134
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133
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<pre style="margin: 0;"> <span id="LC133" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="174" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -175,11 +174,11 @@ int main(int argc, char *argv[])</td>
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175
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174
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<pre style="margin: 0;"> <span id="LC174" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">h</span><span class="p">.</span><span class="n" style="color: #333;">n</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="p">{</span></span>
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176
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175
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<pre style="margin: 0;"> <span id="LC175" class="line" lang="c"> <span class="n" style="color: #333;">dt_hit_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">p</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">h</span><span class="p">.</span><span class="n" style="color: #333;">a</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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177
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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;">double</span> <span class="n" style="color: #333;">x0</span><span class="p">,</span> <span class="n" style="color: #333;">y0</span><span class="p">,</span> <span class="n" style="color: #333;">x1</span><span class="p">,</span> <span class="n" style="color: #333;">y1</span><span class="p">;</span></span>
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178
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<pre style="margin: 0;">-<span id="LC178" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">xo</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">acclen</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="n" style="color: #333;">p</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;"><span class="idiff left">qn</span></span><span class="p"><span class="idiff">],</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">yo</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">acclen</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">][</span></span><span class="n" style="color: #333;"><span class="idiff">p</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff right">t</span>n</span><span class="p">];</span></span>
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177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">xo</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">acclen</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="n" style="color: #333;">p</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;"><span class="idiff left">tn</span></span><span class="p"><span class="idiff">],</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">yo</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">acclen</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">][</span></span><span class="n" style="color: #333;"><span class="idiff">p</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff right">q</span>n</span><span class="p">];</span></span>
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179
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178
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<pre style="margin: 0;"> <span id="LC178" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</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="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">p</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">ts</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">p</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">te</span><span class="p">)</span> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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180
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179
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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;">j</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">p</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">ts</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">p</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">te</span><span class="p">)</span> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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181
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<pre style="margin: 0;">-<span id="LC181" class="line" lang="c"> <span class="n" style="color: #333;">x0</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">p</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;"><span class="idiff left">qs</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">xo</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">sx</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">y0</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">p</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff right">t</span>s</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">yo</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">sy</span><span class="p">;</span></span>
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182
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<pre style="margin: 0;">-<span id="LC182" class="line" lang="c"> <span class="n" style="color: #333;">x1</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">p</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;"><span class="idiff left">qe</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">xo</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">sx</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">y1</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">p</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff right">t</span>e</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">yo</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">sy</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="c"> <span class="n" style="color: #333;">x0</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">p</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;"><span class="idiff left">ts</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">xo</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">sx</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">y0</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">p</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff right">q</span>s</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">yo</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">sy</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="c"> <span class="n" style="color: #333;">x1</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">p</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;"><span class="idiff left">te</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">xo</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">sx</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">y1</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">p</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff right">q</span>e</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">yo</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">sy</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC182" class="line" lang="c"> <span class="n" style="color: #333;">eps_line</span><span class="p">(</span><span class="n" style="color: #333;">stdout</span><span class="p">,</span> <span class="n" style="color: #333;">x0</span><span class="p">,</span> <span class="n" style="color: #333;">y0</span><span class="p">,</span> <span class="n" style="color: #333;">x1</span><span class="p">,</span> <span class="n" style="color: #333;">y1</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC183" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC184" class="line" lang="c"> <span class="n" style="color: #333;">eps_stroke</span><span class="p">(</span><span class="n" style="color: #333;">stdout</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">@@ -14,12 +14,14 @@ KRADIX_SORT_INIT(hit, ma_hit_t, ma_hit_key, 8)</td>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="c"><span class="n" style="color: #333;">KSORT_INIT_GENERIC</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="c"><span class="k" style="font-weight: 600;">typedef</span> <span class="n" style="color: #333;">kvec_t</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="p">)</span> <span class="n" style="color: #333;">uint32_v</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">ma_hit_sort</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">n</span><span class="p">,</span> <span class="n" style="color: #333;">ma_hit_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">a</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="c"><span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="c"> <span class="n" style="color: #333;">radix_sort_hit</span><span class="p">(</span><span class="n" style="color: #333;">a</span><span class="p">,</span> <span class="n" style="color: #333;">a</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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<pre style="margin: 0;"> <span id="LC22" class="line" lang="c"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC23" 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;">void</span> <span class="n" style="color: #333;">ma_hit_mark_unused</span><span class="p">(</span><span class="n" style="color: #333;">sdict_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">d</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right">in</span>t</span> <span class="n" style="color: #333;">n</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">ma_hit_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">a</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;">void</span> <span class="nf" style="color: #900; font-weight: 600;">ma_hit_mark_unused</span><span class="p">(</span><span class="n" style="color: #333;">sdict_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">d</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right">size_</span>t</span> <span class="n" style="color: #333;">n</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">ma_hit_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">a</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="c"><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;">size_t</span> <span class="n" style="color: #333;">i</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">n_seq</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>
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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">@@ -33,7 +35,39 @@ void ma_hit_mark_unused(sdict_t *d, int n, const ma_hit_t *a)</td>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="c"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="c"><span class="n" style="color: #333;">ma_hit_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">ma_hit_read</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;">fn</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">min_span</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">min_match</span><span class="p">,</span> <span class="n" style="color: #333;">sdict_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">d</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">n</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">bi_dir</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="c"><span class="n" style="color: #333;">sdict_t</span> <span class="o" style="font-weight: 600;">*</span><span class="nf" style="color: #900; font-weight: 600;">ma_hit_no_cont</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;">fn</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">min_span</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">min_match</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">max_hang</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">int_frac</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="c"><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;">paf_file_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fp</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;">paf_rec_t</span> <span class="n" style="color: #333;">r</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="c"> <span class="n" style="color: #333;">sdict_t</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="LC43" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="c"> <span class="n" style="color: #333;">fp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">paf_open</span><span class="p">(</span><span class="n" style="color: #333;">fn</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC45" 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;">fp</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"[E::%s] could not open PAF file %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;">__func__</span><span class="p">,</span> <span class="n" style="color: #333;">fn</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="c"> <span class="n" style="color: #333;">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="LC48" class="line" lang="c"> <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;">d</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sd_init</span><span class="p">();</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="c"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">paf_read</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">r</span><span class="p">)</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">l5</span><span class="p">,</span> <span class="n" style="color: #333;">l3</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;">if</span> <span class="p">(</span><span class="n" style="color: #333;">r</span><span class="p">.</span><span class="n" style="color: #333;">qe</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">r</span><span class="p">.</span><span class="n" style="color: #333;">qs</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">min_span</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">r</span><span class="p">.</span><span class="n" style="color: #333;">te</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">r</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;">min_span</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">r</span><span class="p">.</span><span class="n" style="color: #333;">ml</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">min_match</span><span class="p">)</span> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="c"> <span class="n" style="color: #333;">l5</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">r</span><span class="p">.</span><span class="n" style="color: #333;">rev</span><span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">r</span><span class="p">.</span><span class="n" style="color: #333;">tl</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">r</span><span class="p">.</span><span class="n" style="color: #333;">te</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">r</span><span class="p">.</span><span class="n" style="color: #333;">ts</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;">l3</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">r</span><span class="p">.</span><span class="n" style="color: #333;">rev</span><span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">r</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;">r</span><span class="p">.</span><span class="n" style="color: #333;">tl</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">r</span><span class="p">.</span><span class="n" style="color: #333;">te</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="55" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">r</span><span class="p">.</span><span class="n" style="color: #333;">ql</span><span class="o" style="font-weight: 600;">>></span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">r</span><span class="p">.</span><span class="n" style="color: #333;">tl</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="56" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">l5</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">max_hang</span><span class="o" style="font-weight: 600;">>></span><span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">l3</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">max_hang</span><span class="o" style="font-weight: 600;">>></span><span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">r</span><span class="p">.</span><span class="n" style="color: #333;">te</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">r</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;">r</span><span class="p">.</span><span class="n" style="color: #333;">tl</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">int_frac</span><span class="p">)</span> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// internal match</span></span>
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<td class="diff-line-num new new_line" data-linenumber="57" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)</span><span class="n" style="color: #333;">r</span><span class="p">.</span><span class="n" style="color: #333;">qs</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">l5</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">max_hang</span><span class="o" style="font-weight: 600;"><<</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)(</span><span class="n" style="color: #333;">r</span><span class="p">.</span><span class="n" style="color: #333;">ql</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">r</span><span class="p">.</span><span class="n" style="color: #333;">qe</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">l3</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">max_hang</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="58" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="c"> <span class="n" style="color: #333;">sd_put</span><span class="p">(</span><span class="n" style="color: #333;">d</span><span class="p">,</span> <span class="n" style="color: #333;">r</span><span class="p">.</span><span class="n" style="color: #333;">tn</span><span class="p">,</span> <span class="n" style="color: #333;">r</span><span class="p">.</span><span class="n" style="color: #333;">tl</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;">r</span><span class="p">.</span><span class="n" style="color: #333;">ql</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">r</span><span class="p">.</span><span class="n" style="color: #333;">tl</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="60" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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;">r</span><span class="p">.</span><span class="n" style="color: #333;">qs</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">max_hang</span><span class="o" style="font-weight: 600;">>></span><span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">r</span><span class="p">.</span><span class="n" style="color: #333;">ql</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">r</span><span class="p">.</span><span class="n" style="color: #333;">qe</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">max_hang</span><span class="o" style="font-weight: 600;">>></span><span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">r</span><span class="p">.</span><span class="n" style="color: #333;">qe</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">r</span><span class="p">.</span><span class="n" style="color: #333;">qs</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">r</span><span class="p">.</span><span class="n" style="color: #333;">ql</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">int_frac</span><span class="p">)</span> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// internal</span></span>
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<td class="diff-line-num new new_line" data-linenumber="61" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">l5</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="p">)</span><span class="n" style="color: #333;">r</span><span class="p">.</span><span class="n" style="color: #333;">qs</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">max_hang</span><span class="o" style="font-weight: 600;"><<</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">l3</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="p">)(</span><span class="n" style="color: #333;">r</span><span class="p">.</span><span class="n" style="color: #333;">ql</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">r</span><span class="p">.</span><span class="n" style="color: #333;">qe</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">max_hang</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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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="c"> <span class="n" style="color: #333;">sd_put</span><span class="p">(</span><span class="n" style="color: #333;">d</span><span class="p">,</span> <span class="n" style="color: #333;">r</span><span class="p">.</span><span class="n" style="color: #333;">qn</span><span class="p">,</span> <span class="n" style="color: #333;">r</span><span class="p">.</span><span class="n" style="color: #333;">ql</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="c"> <span class="p">}</span></span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="c"> <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="n" style="color: #333;">paf_close</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><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="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">ma_verbose</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;">3</span><span class="p">)</span> <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;">"[M::%s::%s] dropped %d contained reads</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;">__func__</span><span class="p">,</span> <span class="n" style="color: #333;">sys_timestamp</span><span class="p">(),</span> <span class="n" style="color: #333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">n_seq</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="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">d</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="p">}</span></span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="c"></span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="c"><span class="n" style="color: #333;">ma_hit_t</span> <span class="o" style="font-weight: 600;">*</span><span class="nf" style="color: #900; font-weight: 600;">ma_hit_read</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;">fn</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">min_span</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">min_match</span><span class="p">,</span> <span class="n" style="color: #333;">sdict_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">d</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">n</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">bi_dir</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">sdict_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">excl</span><span class="p">)</span></span>
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37
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71
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="c"><span class="p">{</span></span>
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38
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72
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="c"> <span class="n" style="color: #333;">paf_file_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fp</span><span class="p">;</span></span>
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39
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73
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="c"> <span class="n" style="color: #333;">paf_rec_t</span> <span class="n" style="color: #333;">r</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_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="diff-line-num unfold js-unfold new_line" data-linenumber="75" style="width: 35px; color: rgba(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">@@ -41,10 +75,15 @@ ma_hit_t *ma_hit_read(const char *fn, int min_span, int min_match, sdict_t *d, s</td>
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41
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75
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">tot</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">tot_len</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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42
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76
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="c"></span>
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43
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77
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="c"> <span class="n" style="color: #333;">fp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">paf_open</span><span class="p">(</span><span class="n" style="color: #333;">fn</span><span class="p">);</span></span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="c"> <span class="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;">fp</span><span class="p">)</span> <span class="p">{</span></span>
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79
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<pre style="margin: 0;">+<span id="LC79" 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;">"[E::%s] could not open PAF file %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;">__func__</span><span class="p">,</span> <span class="n" style="color: #333;">fn</span><span class="p">);</span></span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="c"> <span class="n" style="color: #333;">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="LC81" class="line" lang="c"> <span class="p">}</span></span>
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44
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82
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="c"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">paf_read</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">r</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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45
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83
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="c"> <span class="n" style="color: #333;">ma_hit_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">p</span><span class="p">;</span></span>
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46
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84
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="c"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">tot</span><span class="p">;</span></span>
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47
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<td class="diff-line-num new_line" data-linenumber="85" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
85
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">r</span><span class="p">.</span><span class="n" style="color: #333;">qe</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">r</span><span class="p">.</span><span class="n" style="color: #333;">qs</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">min_span</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">r</span><span class="p">.</span><span class="n" style="color: #333;">te</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">r</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;">min_span</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">r</span><span class="p">.</span><span class="n" style="color: #333;">ml</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">min_match</span><span class="p">)</span> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">excl</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">sd_get</span><span class="p">(</span><span class="n" style="color: #333;">excl</span><span class="p">,</span> <span class="n" style="color: #333;">r</span><span class="p">.</span><span class="n" style="color: #333;">qn</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="n" style="color: #333;">sd_get</span><span class="p">(</span><span class="n" style="color: #333;">excl</span><span class="p">,</span> <span class="n" style="color: #333;">r</span><span class="p">.</span><span class="n" style="color: #333;">tn</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="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC87" class="line" lang="c"> <span class="n" style="color: #333;">kv_pushp</span><span class="p">(</span><span class="n" style="color: #333;">ma_hit_t</span><span class="p">,</span> <span class="n" style="color: #333;">h</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">p</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="c"> <span class="n" style="color: #333;">p</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">qns</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">uint64_t</span><span class="p">)</span><span class="n" style="color: #333;">sd_put</span><span class="p">(</span><span class="n" style="color: #333;">d</span><span class="p">,</span> <span class="n" style="color: #333;">r</span><span class="p">.</span><span class="n" style="color: #333;">qn</span><span class="p">,</span> <span class="n" style="color: #333;">r</span><span class="p">.</span><span class="n" style="color: #333;">ql</span><span class="p">)</span><span class="o" style="font-weight: 600;"><<</span><span class="mi" style="color: #099;">32</span> <span class="o" style="font-weight: 600;">|</span> <span class="n" style="color: #333;">r</span><span class="p">.</span><span class="n" style="color: #333;">qs</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC89" class="line" lang="c"> <span class="n" style="color: #333;">p</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">qe</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">r</span><span class="p">.</span><span class="n" style="color: #333;">qe</span><span class="p">;</span></span>
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<a href="https://salsa.debian.org/med-team/miniasm/compare/c23b2121ec3f8082bbb02499edea827181a76fda...d7b6c4f3557ddd7602088589e02ff4ef9e874444#406e031b8824ea26ae0bf4d7579a1d89e3fb5906"><strong>main.c</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -8,7 +8,7 @@</td>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "sdict.h"</span></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "miniasm.h"</span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define MA_VERSION "0.<span class="idiff left right">2-r128</span>"</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define MA_VERSION "0.<span class="idiff left right">3-r179</span>"</span></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">print_subs</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">sdict_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">d</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">ma_sub_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">sub</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="c"><span class="p">{</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -32,16 +32,16 @@ static void print_hits(size_t n_hits, const ma_hit_t *hit, const sdict_t *d, con</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;">int</span> <span class="nf" style="color: #900; font-weight: 600;">main</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">argc</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">argv</span><span class="p">[])</span></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="c"><span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="c"> <span class="n" style="color: #333;">ma_opt_t</span> <span class="n" style="color: #333;">opt</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">c</span><span class="p">,</span> <span class="n" style="color: #333;">stage</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">100</span><span class="p">,</span> <span class="n" style="color: #333;">no_first</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;">no_second</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;">bi_dir</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;">o_set</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="LC36" class="line" lang="c"> <span class="n" style="color: #333;">sdict_t</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="LC35" 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;">c</span><span class="p">,</span> <span class="n" style="color: #333;">stage</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">100</span><span class="p">,</span> <span class="n" style="color: #333;">no_first</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;">no_second</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;">bi_dir</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;">o_set</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">no_cont</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 right">0</span></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;">sdict_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">d</span><span class="p"><span class="idiff left">,</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">excl</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 right">0</span></span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="c"> <span class="n" style="color: #333;">ma_sub_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">sub</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="LC38" class="line" lang="c"> <span class="n" style="color: #333;">ma_hit_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">hit</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">n_hits</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">cov</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">cov</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">40</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="LC41" 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;">fn_reads</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;">outfmt</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"ug"</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="c"> <span class="n" style="color: #333;">ma_opt_init</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">opt</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="c"> <span class="k" style="font-weight: 600;">while</span> <span class="p">((</span><span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">getopt</span><span class="p">(</span><span class="n" style="color: #333;">argc</span><span class="p">,</span> <span class="n" style="color: #333;">argv</span><span class="p">,</span> <span class="s" style="color: #d14;">"n:m:s:c:<span class="idiff left right">C:S:i:d:g:o:h:I:r:f:e:p:12VB</span>bF:"</span><span class="p">))</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="c"> <span class="k" style="font-weight: 600;">while</span> <span class="p">((</span><span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">getopt</span><span class="p">(</span><span class="n" style="color: #333;">argc</span><span class="p">,</span> <span class="n" style="color: #333;">argv</span><span class="p">,</span> <span class="s" style="color: #d14;">"n:m:s:c:<span class="idiff left right">S:i:d:g:o:h:I:r:f:e:p:12VBR</span>bF:"</span><span class="p">))</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'m'</span><span class="p">)</span> <span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">min_match</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">atoi</span><span class="p">(</span><span class="n" style="color: #333;">optarg</span><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;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'i'</span><span class="p">)</span> <span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">min_iden</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">atof</span><span class="p">(</span><span class="n" style="color: #333;">optarg</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="c"> <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;">c</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'s'</span><span class="p">)</span> <span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">min_span</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">atoi</span><span class="p">(</span><span class="n" style="color: #333;">optarg</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">@@ -58,9 +58,9 @@ int main(int argc, char *argv[])</td>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="c"> <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;">c</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'1'</span><span class="p">)</span> <span class="n" style="color: #333;">no_first</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="LC59" class="line" lang="c"> <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;">c</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'2'</span><span class="p">)</span> <span class="n" style="color: #333;">no_second</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="60" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
60
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<td class="diff-line-num new_line" data-linenumber="60" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
60
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="c"> <span class="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;">c</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'n'</span><span class="p">)</span> <span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">n_rounds</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">atoi</span><span class="p">(</span><span class="n" style="color: #333;">optarg</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 old old_line" data-linenumber="61" 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">
61
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<td class="diff-line-num new_line old" data-linenumber="61" 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="LC61" class="line" lang="c"> <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;">c</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'C'</span><span class="p">)</span> <span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">cov_ratio</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">atof</span><span class="p">(</span><span class="n" style="color: #333;">optarg</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
62
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<td class="diff-line-num new_line" data-linenumber="61" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
61
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="c"> <span class="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;">c</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'B'</span><span class="p">)</span> <span class="n" style="color: #333;">bi_dir</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="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
63
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<td class="diff-line-num new_line" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
62
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="c"> <span class="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;">c</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'b'</span><span class="p">)</span> <span class="n" style="color: #333;">bi_dir</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 old_line" data-linenumber="64" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="c"> <span class="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;">c</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'R'</span><span class="p">)</span> <span class="n" style="color: #333;">no_cont</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="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="c"> <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;">c</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'F'</span><span class="p">)</span> <span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">final_ovlp_drop_ratio</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">atof</span><span class="p">(</span><span class="n" style="color: #333;">optarg</span><span class="p">);</span></span>
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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="c"> <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;">c</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'V'</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="66" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
66
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<td class="diff-line-num new_line" data-linenumber="66" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
66
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="c"> <span class="n" style="color: #333;">printf</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;">MA_VERSION</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="76" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -76,6 +76,7 @@ int main(int argc, char *argv[])</td>
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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">
76
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<td class="diff-line-num new_line" data-linenumber="76" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
76
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<pre style="margin: 0;"> <span id="LC76" 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;">"Usage: miniasm [options] <in.paf></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="77" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
77
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<td class="diff-line-num new_line" data-linenumber="77" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
77
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<pre style="margin: 0;"> <span id="LC77" 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;">"Options:</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="78" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
78
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<td class="diff-line-num new_line" data-linenumber="78" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
78
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">" Pre-selection:</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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<td class="diff-line-num new old_line" data-linenumber="79" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="79" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="c"> <span class="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;">" -R prefilter clearly contained reads (2-pass required)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="79" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
79
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<td class="diff-line-num new_line" data-linenumber="80" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
80
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">" -m INT min match length [%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;">opt</span><span class="p">.</span><span class="n" style="color: #333;">min_match</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="80" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
80
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<td class="diff-line-num new_line" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
81
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<pre style="margin: 0;"> <span id="LC81" 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;">" -i FLOAT min identity [%.2g]</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;">opt</span><span class="p">.</span><span class="n" style="color: #333;">min_iden</span><span class="p">);</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
81
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<td class="diff-line-num new_line" data-linenumber="82" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
82
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">" -s INT min span [%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;">opt</span><span class="p">.</span><span class="n" style="color: #333;">min_span</span><span class="p">);</span></span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="107" style="width: 35px; color: rgba(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">@@ -107,8 +108,13 @@ int main(int argc, char *argv[])</td>
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107
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<td class="diff-line-num 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">
108
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<pre style="margin: 0;"> <span id="LC108" class="line" lang="c"> <span class="n" style="color: #333;">sys_init</span><span class="p">();</span></span>
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108
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109
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<pre style="margin: 0;"> <span id="LC109" class="line" lang="c"> <span class="n" style="color: #333;">d</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sd_init</span><span class="p">();</span></span>
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109
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110
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<pre style="margin: 0;"> <span id="LC110" class="line" lang="c"></span>
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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;">no_cont</span><span class="p">)</span> <span class="p">{</span></span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"[M::%s] ===> Step 0: removing contained reads <===</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;">__func__</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="113" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="c"> <span class="n" style="color: #333;">excl</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ma_hit_no_cont</span><span class="p">(</span><span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="n" style="color: #333;">optind</span><span class="p">],</span> <span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">min_span</span><span class="p">,</span> <span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">min_match</span><span class="p">,</span> <span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">max_hang</span><span class="p">,</span> <span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">int_frac</span><span class="p">);</span></span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="c"> <span class="p">}</span></span>
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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="c"></span>
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110
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116
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<pre style="margin: 0;"> <span id="LC116" 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;">"[M::%s] ===> Step 1: reading read mappings <===</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;">__func__</span><span class="p">);</span></span>
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111
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<pre style="margin: 0;">-<span id="LC111" class="line" lang="c"> <span class="n" style="color: #333;">hit</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ma_hit_read</span><span class="p">(</span><span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="n" style="color: #333;">optind</span><span class="p">],</span> <span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">min_span</span><span class="p">,</span> <span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">min_match</span><span class="p">,</span> <span class="n" style="color: #333;">d</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">n_hits</span><span class="p">,</span> <span class="n" style="color: #333;">bi_dir</span><span class="p">);</span></span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="c"> <span class="n" style="color: #333;">hit</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ma_hit_read</span><span class="p">(</span><span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="n" style="color: #333;">optind</span><span class="p">],</span> <span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">min_span</span><span class="p">,</span> <span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">min_match</span><span class="p">,</span> <span class="n" style="color: #333;">d</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">n_hits</span><span class="p">,</span> <span class="n" style="color: #333;">bi_dir</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">excl</span></span><span class="p">);</span></span>
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112
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118
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<pre style="margin: 0;"> <span id="LC118" class="line" lang="c"></span>
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113
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119
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<pre style="margin: 0;"> <span id="LC119" 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;">no_first</span><span class="p">)</span> <span class="p">{</span></span>
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114
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120
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<pre style="margin: 0;"> <span id="LC120" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"[M::%s] ===> Step 2: 1-pass (crude) read selection <===</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;">__func__</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="123" style="width: 35px; color: rgba(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="129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -123,12 +129,14 @@ int main(int argc, char *argv[])</td>
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123
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129
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<pre style="margin: 0;"> <span id="LC129" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"[M::%s] ===> Step 3: 2-pass (fine) read selection <===</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;">__func__</span><span class="p">);</span></span>
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124
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130
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<pre style="margin: 0;"> <span id="LC130" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">stage</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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125
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131
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<pre style="margin: 0;"> <span id="LC131" class="line" lang="c"> <span class="n" style="color: #333;">ma_sub_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">sub2</span><span class="p">;</span></span>
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126
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<pre style="margin: 0;">-<span id="LC126" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">min_dp</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="p">)(</span><span class="n" style="color: #333;">cov</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">cov_ratio</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">.</span><span class="mi" style="color: #099;">499</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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127
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<pre style="margin: 0;">-<span id="LC127" class="line" lang="c"> <span class="n" style="color: #333;">min_dp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">min_dp</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">min_dp</span><span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">min_dp</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">min_dp</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC128" class="line" lang="c"> <span class="n" style="color: #333;">sub2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ma_hit_sub</span><span class="p">(</span><span class="n" style="color: #333;">min_dp</span><span class="p">,</span> <span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">min_iden</span><span class="p">,</span> <span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">min_span</span><span class="o" style="font-weight: 600;">/</span><span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="n" style="color: #333;">n_hits</span><span class="p">,</span> <span class="n" style="color: #333;">hit</span><span class="p">,</span> <span class="n" style="color: #333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">n_seq</span><span class="p">);</span></span>
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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="c"> <span class="n" style="color: #333;">sub2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ma_hit_sub</span><span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">min_dp</span><span class="p">,</span> <span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">min_iden</span><span class="p">,</span> <span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">min_span</span><span class="o" style="font-weight: 600;">/</span><span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="n" style="color: #333;">n_hits</span><span class="p">,</span> <span class="n" style="color: #333;">hit</span><span class="p">,</span> <span class="n" style="color: #333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">n_seq</span><span class="p">);</span></span>
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129
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133
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<pre style="margin: 0;"> <span id="LC133" class="line" lang="c"> <span class="n" style="color: #333;">n_hits</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ma_hit_cut</span><span class="p">(</span><span class="n" style="color: #333;">sub2</span><span class="p">,</span> <span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">min_span</span><span class="p">,</span> <span class="n" style="color: #333;">n_hits</span><span class="p">,</span> <span class="n" style="color: #333;">hit</span><span class="p">);</span></span>
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130
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<pre style="margin: 0;">-<span id="LC130" class="line" lang="c"> <span class="n" style="color: #333;">ma_sub_merge</span><span class="p">(</span><span class="n" style="color: #333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">n_seq</span><span class="p">,</span> <span class="n" style="color: #333;">sub</span><span class="p">,</span> <span class="n" style="color: #333;">sub2</span><span class="p">);</span></span>
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131
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<pre style="margin: 0;">-<span id="LC131" class="line" lang="c"> <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">sub2</span><span class="p">);</span></span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="c"> <span class="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;">no_first</span><span class="p">)</span> <span class="p">{</span></span>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="c"> <span class="n" style="color: #333;">ma_sub_merge</span><span class="p">(</span><span class="n" style="color: #333;">d</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">n_seq</span><span class="p">,</span> <span class="n" style="color: #333;">sub</span><span class="p">,</span> <span class="n" style="color: #333;">sub2</span><span class="p">);</span></span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="c"> <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">sub2</span><span class="p">);</span></span>
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137
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<pre style="margin: 0;">+<span id="LC137" 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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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="c"> <span class="n" style="color: #333;">sub</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sub2</span><span class="p">;</span></span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="c"> <span class="p">}</span></span>
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132
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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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133
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141
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<pre style="margin: 0;"> <span id="LC141" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">stage</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;">5</span><span class="p">)</span> <span class="n" style="color: #333;">n_hits</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ma_hit_contained</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">opt</span><span class="p">,</span> <span class="n" style="color: #333;">d</span><span class="p">,</span> <span class="n" style="color: #333;">sub</span><span class="p">,</span> <span class="n" style="color: #333;">n_hits</span><span class="p">,</span> <span class="n" style="color: #333;">hit</span><span class="p">);</span></span>
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134
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142
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<pre style="margin: 0;"> <span id="LC142" 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="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="147" style="width: 35px; color: rgba(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">@@ -139,7 +147,7 @@ int main(int argc, char *argv[])</td>
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139
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147
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<pre style="margin: 0;"> <span id="LC147" class="line" lang="c"> <span class="n" style="color: #333;">print_subs</span><span class="p">(</span><span class="n" style="color: #333;">d</span><span class="p">,</span> <span class="n" style="color: #333;">sub</span><span class="p">);</span></span>
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140
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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="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;">outfmt</span><span class="p">,</span> <span class="s" style="color: #d14;">"paf"</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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141
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149
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<pre style="margin: 0;"> <span id="LC149" class="line" lang="c"> <span class="n" style="color: #333;">print_hits</span><span class="p">(</span><span class="n" style="color: #333;">n_hits</span><span class="p">,</span> <span class="n" style="color: #333;">hit</span><span class="p">,</span> <span class="n" style="color: #333;">d</span><span class="p">,</span> <span class="n" style="color: #333;">sub</span><span class="p">);</span></span>
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142
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<pre style="margin: 0;">-<span id="LC142" class="line" lang="c"> <span class="p">}</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;">outfmt</span><span class="p">,</span> <span class="s" style="color: #d14;">"ug"</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="n" style="color: #333;">strcmp</span><span class="p">(</span><span class="n" style="color: #333;">outfmt</span><span class="p">,</span> <span class="s" style="color: #d14;">"sg"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="150" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;"><span class="idiff left">else</span></span><span class="idiff right"> </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;">outfmt</span><span class="p">,</span> <span class="s" style="color: #d14;">"ug"</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="n" style="color: #333;">strcmp</span><span class="p">(</span><span class="n" style="color: #333;">outfmt</span><span class="p">,</span> <span class="s" style="color: #d14;">"sg"</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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143
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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;">asg_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">sg</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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144
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152
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<pre style="margin: 0;"> <span id="LC152" class="line" lang="c"> <span class="n" style="color: #333;">ma_ug_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">ug</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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145
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153
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<pre style="margin: 0;"> <span id="LC153" class="line" lang="c"></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="200" style="width: 35px; color: rgba(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 +200,7 @@ int main(int argc, char *argv[])</td>
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192
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200
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<pre style="margin: 0;"> <span id="LC200" class="line" lang="c"></span>
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<td class="diff-line-num old_line" data-linenumber="193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
193
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<td class="diff-line-num new_line" data-linenumber="201" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
201
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<pre style="margin: 0;"> <span id="LC201" class="line" lang="c"> <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">sub</span><span class="p">);</span> <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">hit</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="194" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
194
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202
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<pre style="margin: 0;"> <span id="LC202" class="line" lang="c"> <span class="n" style="color: #333;">sd_destroy</span><span class="p">(</span><span class="n" style="color: #333;">d</span><span class="p">);</span></span>
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203
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">excl</span><span class="p">)</span> <span class="n" style="color: #333;">sd_destroy</span><span class="p">(</span><span class="n" style="color: #333;">excl</span><span class="p">);</span></span>
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195
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204
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<pre style="margin: 0;"> <span id="LC204" class="line" lang="c"></span>
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196
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205
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<pre style="margin: 0;"> <span id="LC205" 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;">"[M::%s] Version: %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;">__func__</span><span class="p">,</span> <span class="n" style="color: #333;">MA_VERSION</span><span class="p">);</span></span>
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197
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206
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<pre style="margin: 0;"> <span id="LC206" 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;">"[M::%s] CMD:"</span><span class="p">,</span> <span class="n" style="color: #333;">__func__</span><span class="p">);</span></span>
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<a href="https://salsa.debian.org/med-team/miniasm/compare/c23b2121ec3f8082bbb02499edea827181a76fda...d7b6c4f3557ddd7602088589e02ff4ef9e874444#bb2117c4db3ac04cd9d344fb347a1ff30181fa06"><strong>miniasm.1</strong></a>
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1
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">.TH mini<span class="idiff left right">map 1 "06 December 2015" "miniasm-0.2</span>" "Bioinformatics tools"</span>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">.TH mini<span class="idiff left right">asm 1 "23 July 2018" "miniasm-0.3 (r179)</span>" "Bioinformatics tools"</span>
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2
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"></span>
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3
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">.SH NAME</span>
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<td class="diff-line-num old_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">
4
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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">
4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">.PP</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="7" style="width: 35px; color: rgba(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="7" style="width: 35px; color: rgba(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">@@ -7,7 +7,7 @@ miniasm - de novo assembler for long read sequences</td>
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7
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7
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">.SH SYNOPSIS</span>
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<td class="diff-line-num old_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
8
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<td class="diff-line-num new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
8
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">.PP</span>
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9
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<td class="diff-line-num new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
9
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">miniasm</span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext">.RB [ -b12V ]</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">.RB [ -b12V<span class="idiff left right">R</span> ]</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">.RB [ -m</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">.IR minMatch ]</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">.RB [ -i</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">@@ -56,6 +56,21 @@ to the raw input reads.</td>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="plaintext">.SS Preselection options</span>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="plaintext">.TP 10</span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="plaintext">.BI -R</span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="plaintext">Pre-filter clearly contained short reads. In this mode,</span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="plaintext">.I mapping.paf</span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="plaintext">is read twice. The first pass identifies contained reads without loading hits</span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="plaintext">to RAM; the second pass skips contained reads and load the rest into RAM. Due</span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="plaintext">to the 2-pass behavior, the peak RAM is greatly reduced, but</span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="plaintext">.I mapping.paf</span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="plaintext">has to be a normal file, not a stream. When this option is in use, it is</span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="plaintext">recommended to reduce</span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="plaintext">.B -c</span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="plaintext">to 2, as there are fewer reads after pre-filtering. Applying</span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="plaintext">.BI -Rc 2</span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="plaintext">sometimes improves assembly.</span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="plaintext">.BI -m \ INT</span>
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="plaintext">Drop mappings having less than</span>
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="plaintext">.I INT</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">@@ -231,9 +246,20 @@ _</td>
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<pre style="margin: 0;"> <span id="LC246" class="line" lang="plaintext">H Header N/A</span>
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<pre style="margin: 0;"> <span id="LC247" class="line" lang="plaintext">S Segment segName segSeq</span>
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<pre style="margin: 0;"> <span id="LC248" class="line" lang="plaintext">L Overlap segName1 segOri1 segName2 segOri2 ovlpCIGAR</span>
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<pre style="margin: 0;">-<span id="LC234" class="line" lang="plaintext">a Golden path utgName utgStart readName:<span class="idiff left right">start-end readOri length</span></span>
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<pre style="margin: 0;">+<span id="LC249" class="line" lang="plaintext">a Golden path utgName utgStart readName:<span class="idiff left right">rStart-rEnd readOri incLen</span></span>
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<pre style="margin: 0;"> <span id="LC250" class="line" lang="plaintext">.TE</span>
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<pre style="margin: 0;"> <span id="LC251" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC252" class="line" lang="plaintext">.PP</span>
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<pre style="margin: 0;">+<span id="LC253" class="line" lang="plaintext">An `a' line indicates that the unitig subsequence in</span>
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<pre style="margin: 0;">+<span id="LC254" class="line" lang="plaintext">.RI [ utgStart , utgStart + incLen )</span>
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<pre style="margin: 0;">+<span id="LC255" class="line" lang="plaintext">is taken from read</span>
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<pre style="margin: 0;">+<span id="LC256" class="line" lang="plaintext">.I readName</span>
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<pre style="margin: 0;">+<span id="LC257" class="line" lang="plaintext">in region</span>
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<pre style="margin: 0;">+<span id="LC258" class="line" lang="plaintext">.RI [ rStart -1, rStart -1+ incLen ).</span>
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<pre style="margin: 0;">+<span id="LC259" class="line" lang="plaintext">It is not a</span>
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<pre style="margin: 0;">+<span id="LC260" class="line" lang="plaintext">standard GFA line. An `x' line gives a brief summary of each unitig, which can</span>
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<pre style="margin: 0;">+<span id="LC261" class="line" lang="plaintext">be inferred from `S' and `a' lines.</span>
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<pre style="margin: 0;">+<span id="LC262" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC263" class="line" lang="plaintext">.SH SEE ALSO</span>
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<pre style="margin: 0;"> <span id="LC264" class="line" lang="plaintext">.PP</span>
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<pre style="margin: 0;"> <span id="LC265" class="line" lang="plaintext">minimap(1)</span></pre>
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<li id="6091887a096fc27c98e524e1c34ccdb367c5703d">
<a href="https://salsa.debian.org/med-team/miniasm/compare/c23b2121ec3f8082bbb02499edea827181a76fda...d7b6c4f3557ddd7602088589e02ff4ef9e874444#6091887a096fc27c98e524e1c34ccdb367c5703d"><strong>miniasm.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">@@ -14,7 +14,6 @@ typedef struct {</td>
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14
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">min_match</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">min_dp</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">min_iden</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">cov_ratio</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">max_hang</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">min_ovlp</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">@@ -60,7 +59,8 @@ extern "C" {</td>
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<pre style="margin: 0;"> <span id="LC59" 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="LC60" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">ma_opt_init</span><span class="p">(</span><span class="n" style="color: #333;">ma_opt_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">opt</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="c"><span class="n" style="color: #333;">ma_hit_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">ma_hit_read</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;">fn</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">min_span</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">min_match</span><span class="p">,</span> <span class="n" style="color: #333;">sdict_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">d</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">n</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">bi_dir</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="c"><span class="n" style="color: #333;">sdict_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">ma_hit_no_cont</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;">fn</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">min_span</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">min_match</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">max_hang</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">int_frac</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="c"><span class="n" style="color: #333;">ma_hit_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">ma_hit_read</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;">fn</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">min_span</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">min_match</span><span class="p">,</span> <span class="n" style="color: #333;">sdict_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">d</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">n</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">bi_dir</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">sdict_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">excl</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="c"><span class="n" style="color: #333;">ma_sub_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">ma_hit_sub</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">min_dp</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">min_iden</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">end_clip</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">n</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">ma_hit_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">a</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">n_sub</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">ma_hit_cut</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">ma_sub_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">reg</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">min_span</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">n</span><span class="p">,</span> <span class="n" style="color: #333;">ma_hit_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">a</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">ma_hit_flt</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">ma_sub_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">sub</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">max_hang</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">min_ovlp</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">n</span><span class="p">,</span> <span class="n" style="color: #333;">ma_hit_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">a</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">cov</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">@@ -87,7 +87,6 @@ static inline int ma_hit2arc(const ma_hit_t *h, int ql, int tl, int max_hang, fl</td>
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<pre style="margin: 0;"> <span id="LC87" class="line" lang="c"><span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">tl5</span><span class="p">,</span> <span class="n" style="color: #333;">tl3</span><span class="p">,</span> <span class="n" style="color: #333;">ext5</span><span class="p">,</span> <span class="n" style="color: #333;">ext3</span><span class="p">,</span> <span class="n" style="color: #333;">qs</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int32_t</span><span class="p">)</span><span class="n" style="color: #333;">h</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">qns</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC89" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">u</span><span class="p">,</span> <span class="n" style="color: #333;">v</span><span class="p">,</span> <span class="n" style="color: #333;">l</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// u: query end; v: target end; l: length from u to v</span></span>
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<pre style="margin: 0;">-<span id="LC90" 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;">v</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">l</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">UINT32_MAX</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">h</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">rev</span><span class="p">)</span> <span class="n" style="color: #333;">tl5</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tl</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">h</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">te</span><span class="p">,</span> <span class="n" style="color: #333;">tl3</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">h</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">ts</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// tl5: 5'-end overhang (on the query strand); tl3: similar</span></span>
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">tl5</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">h</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;">tl3</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tl</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">h</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">te</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="c"> <span class="n" style="color: #333;">ext5</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">qs</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">tl5</span><span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">qs</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">tl5</span><span class="p">;</span></span>
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<a href="https://salsa.debian.org/med-team/miniasm/compare/c23b2121ec3f8082bbb02499edea827181a76fda...d7b6c4f3557ddd7602088589e02ff4ef9e874444#147dae8884008957fecbb07b1b51ec7cb51a9644"><strong>misc/da2paf.pl</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -5,19 +5,23 @@ use warnings;</td>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nn" style="color: #555;">Getopt::</span><span class="nv" style="color: teal;">Std</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="perl"></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="o" style="font-weight: 600;">%</span><span class="nv" style="color: teal;">opts</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="perl"><span class="nv" style="color: teal;">getopts</span><span class="p">(</span><span class="s" style="color: #d14;">"2"</span><span class="p">,</span> <span class="o" style="font-weight: 600;">\%</span><span class="nv" style="color: teal;">opts</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="perl"><span class="nb" style="color: #0086b3;">die</span><span class="p">(</span><span class="s" style="color: #d14;">"Usage: ls *.las | xargs -i LAdump -cd reads.db {} | da2paf.pl [-2] <(DBdump -rh reads.db)\n"</span><span class="p">)</span> <span class="k" style="font-weight: 600;">if</span> <span class="nv" style="color: teal;">@ARGV</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="LC8" class="line" lang="perl"><span class="nv" style="color: teal;">getopts</span><span class="p">(</span><span class="s" style="color: #d14;">"2<span class="idiff left right">n</span>"</span><span class="p">,</span> <span class="o" style="font-weight: 600;">\%</span><span class="nv" style="color: teal;">opts</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="perl"><span class="nb" style="color: #0086b3;">die</span><span class="p">(</span><span class="s" style="color: #d14;">"Usage: ls *.las | xargs -i LAdump -cd reads.db {} | da2paf.pl [-2<span class="idiff left right">n</span>] <(DBdump -rh reads.db)\n"</span><span class="p">)</span> <span class="k" style="font-weight: 600;">if</span> <span class="nv" style="color: teal;">@ARGV</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="LC10" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$is_dbl</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">defined</span><span class="p">(</span><span class="nv" style="color: teal;">$opts</span><span class="p">{</span><span class="mi" style="color: #099;">2</span><span class="p">});</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$with_name</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">defined</span><span class="p">(</span><span class="nv" style="color: teal;">$opts</span><span class="p">{</span><span class="nv" style="color: teal;">n</span><span class="p">});</span></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="perl"></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="perl"><span class="nb" style="color: #0086b3;">warn</span><span class="p">(</span><span class="s" style="color: #d14;">"Reading sequence lengths...\n"</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$fn</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">shift</span><span class="p">(</span><span class="nv" style="color: teal;">@ARGV</span><span class="p">);</span></span>
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15
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="perl"><span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="nv" style="color: teal;">FH</span><span class="p">,</span> <span class="nv" style="color: teal;">$fn</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="nb" style="color: #0086b3;">die</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="p">(</span><span class="nv" style="color: teal;">$id</span><span class="p">,</span> <span class="nv" style="color: teal;"><span class="idiff left right">@len</span></span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="p">(</span><span class="nv" style="color: teal;">$id</span><span class="p">,</span> <span class="nv" style="color: teal;"><span class="idiff left">$pre</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">@len</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff right">@name</span></span><span class="p">);</span></span>
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16
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17
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="perl"><span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="o" style="font-weight: 600;"><</span><span class="nv" style="color: teal;">FH</span><span class="o" style="font-weight: 600;">></span><span class="p">)</span> <span class="p">{</span></span>
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17
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18
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="sr" style="color: #009926;">/^R\s(\d+)/</span><span class="p">)</span> <span class="p">{</span></span>
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18
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19
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="perl"> <span class="nv" style="color: teal;">$id</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$1</span><span class="p">;</span></span>
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19
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="perl"> <span class="p">}</span> <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="sr" style="color: #009926;">/^L\s\S+\s(\d+)\s(\d+)/</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="perl"> <span class="nv" style="color: teal;">$len</span><span class="p">[</span><span class="nv" style="color: teal;">$id</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$2</span> <span class="o" style="font-weight: 600;">-</span> <span class="nv" style="color: teal;">$1</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="perl"> <span class="p">}</span> <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="sr" style="color: #009926;">/^H\s\S+\s(\S+)/</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="perl"> <span class="nv" style="color: teal;">$pre</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$1</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="perl"> <span class="p">}</span> <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="sr" style="color: #009926;">/^L\s(\S+)\s(\d+)\s(\d+)/</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="perl"> <span class="nv" style="color: teal;">$len</span><span class="p">[</span><span class="nv" style="color: teal;">$id</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$3</span> <span class="o" style="font-weight: 600;">-</span> <span class="nv" style="color: teal;">$2</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="perl"> <span class="nv" style="color: teal;">$name</span><span class="p">[</span><span class="nv" style="color: teal;">$id</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"$pre/$1/$2_$3"</span><span class="p">;</span></span>
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25
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="perl"> <span class="p">}</span></span>
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26
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="perl"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="perl"><span class="nb" style="color: #0086b3;">close</span><span class="p">(</span><span class="nv" style="color: teal;">FH</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -33,11 +37,12 @@ while (<>) {</td>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="perl"> <span class="p">}</span> <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="nv" style="color: teal;">$skip</span> <span class="o" style="font-weight: 600;">&&</span> <span class="sr" style="color: #009926;">/^D\s(\d+)/</span><span class="p">)</span> <span class="p">{</span></span>
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34
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38
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$bl</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$ae</span> <span class="o" style="font-weight: 600;">-</span> <span class="nv" style="color: teal;">$ab</span> <span class="o" style="font-weight: 600;">></span> <span class="nv" style="color: teal;">$be</span> <span class="o" style="font-weight: 600;">-</span> <span class="nv" style="color: teal;">$bb</span><span class="p">?</span> <span class="nv" style="color: teal;">$ae</span> <span class="o" style="font-weight: 600;">-</span> <span class="nv" style="color: teal;">$ab</span> <span class="p">:</span> <span class="nv" style="color: teal;">$be</span> <span class="o" style="font-weight: 600;">-</span> <span class="nv" style="color: teal;">$bb</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$ml</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$bl</span> <span class="o" style="font-weight: 600;">-</span> <span class="nv" style="color: teal;">$1</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="p">(</span><span class="nv" style="color: teal;">$n0</span><span class="p">,</span> <span class="nv" style="color: teal;">$n1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$with_name</span><span class="p">?</span> <span class="p">(</span><span class="nv" style="color: teal;">$name</span><span class="p">[</span><span class="nv" style="color: teal;">$id0</span><span class="p">],</span> <span class="nv" style="color: teal;">$name</span><span class="p">[</span><span class="nv" style="color: teal;">$id1</span><span class="p">])</span> <span class="p">:</span> <span class="p">(</span><span class="nv" style="color: teal;">$id0</span><span class="p">,</span> <span class="nv" style="color: teal;">$id1</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: teal;">$strand</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="s" style="color: #d14;">'+'</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="nb" style="color: #0086b3;">join</span><span class="p">(</span><span class="s" style="color: #d14;">"\t"</span><span class="p">,</span> <span class="nv" style="color: teal;">$<span class="idiff left">id0</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$len</span></span><span class="p"><span class="idiff">[</span></span><span class="nv" style="color: teal;"><span class="idiff">$id0</span></span><span class="p"><span class="idiff">],</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$ab</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$ae</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">'+'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff right">$id</span>1</span><span class="p">,</span> <span class="nv" style="color: teal;">$len</span><span class="p">[</span><span class="nv" style="color: teal;">$id1</span><span class="p">],</span> <span class="nv" style="color: teal;">$bb</span><span class="p">,</span> <span class="nv" style="color: teal;">$be</span><span class="p">,</span> <span class="nv" style="color: teal;">$ml</span><span class="p">,</span> <span class="nv" style="color: teal;">$bl</span><span class="p">,</span> <span class="mi" style="color: #099;">255</span><span class="p">),</span> <span class="s" style="color: #d14;">"\n"</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="nb" style="color: #0086b3;">join</span><span class="p">(</span><span class="s" style="color: #d14;">"\t"</span><span class="p">,</span> <span class="nv" style="color: teal;">$<span class="idiff left">n0</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$len</span></span><span class="p"><span class="idiff">[</span></span><span class="nv" style="color: teal;"><span class="idiff">$id0</span></span><span class="p"><span class="idiff">],</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$ab</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$ae</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">'+'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff right">$n</span>1</span><span class="p">,</span> <span class="nv" style="color: teal;">$len</span><span class="p">[</span><span class="nv" style="color: teal;">$id1</span><span class="p">],</span> <span class="nv" style="color: teal;">$bb</span><span class="p">,</span> <span class="nv" style="color: teal;">$be</span><span class="p">,</span> <span class="nv" style="color: teal;">$ml</span><span class="p">,</span> <span class="nv" style="color: teal;">$bl</span><span class="p">,</span> <span class="mi" style="color: #099;">255</span><span class="p">),</span> <span class="s" style="color: #d14;">"\n"</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="perl"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$l</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$len</span><span class="p">[</span><span class="nv" style="color: teal;">$id1</span><span class="p">];</span></span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="nb" style="color: #0086b3;">join</span><span class="p">(</span><span class="s" style="color: #d14;">"\t"</span><span class="p">,</span> <span class="nv" style="color: teal;">$<span class="idiff left">id0</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$len</span></span><span class="p"><span class="idiff">[</span></span><span class="nv" style="color: teal;"><span class="idiff">$id0</span></span><span class="p"><span class="idiff">],</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$ab</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$ae</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">'-'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff right">$id</span>1</span><span class="p">,</span> <span class="nv" style="color: teal;">$l</span><span class="p">,</span> <span class="nv" style="color: teal;">$l</span> <span class="o" style="font-weight: 600;">-</span> <span class="nv" style="color: teal;">$be</span><span class="p">,</span> <span class="nv" style="color: teal;">$l</span> <span class="o" style="font-weight: 600;">-</span> <span class="nv" style="color: teal;">$bb</span><span class="p">,</span> <span class="nv" style="color: teal;">$ml</span><span class="p">,</span> <span class="nv" style="color: teal;">$bl</span><span class="p">,</span> <span class="mi" style="color: #099;">255</span><span class="p">),</span> <span class="s" style="color: #d14;">"\n"</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="nb" style="color: #0086b3;">join</span><span class="p">(</span><span class="s" style="color: #d14;">"\t"</span><span class="p">,</span> <span class="nv" style="color: teal;">$<span class="idiff left">n0</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$len</span></span><span class="p"><span class="idiff">[</span></span><span class="nv" style="color: teal;"><span class="idiff">$id0</span></span><span class="p"><span class="idiff">],</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$ab</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$ae</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">'-'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff right">$n</span>1</span><span class="p">,</span> <span class="nv" style="color: teal;">$l</span><span class="p">,</span> <span class="nv" style="color: teal;">$l</span> <span class="o" style="font-weight: 600;">-</span> <span class="nv" style="color: teal;">$be</span><span class="p">,</span> <span class="nv" style="color: teal;">$l</span> <span class="o" style="font-weight: 600;">-</span> <span class="nv" style="color: teal;">$bb</span><span class="p">,</span> <span class="nv" style="color: teal;">$ml</span><span class="p">,</span> <span class="nv" style="color: teal;">$bl</span><span class="p">,</span> <span class="mi" style="color: #099;">255</span><span class="p">),</span> <span class="s" style="color: #d14;">"\n"</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="perl"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="perl"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="perl"><span class="p">}</span></span></pre>
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<a href="https://salsa.debian.org/med-team/miniasm/compare/c23b2121ec3f8082bbb02499edea827181a76fda...d7b6c4f3557ddd7602088589e02ff4ef9e874444#22b27b676f55c1a3e373e08746bba43d6414a001"><strong>misc/mhap2paf.pl</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -5,10 +5,21 @@ use warnings;</td>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nn" style="color: #555;">Getopt::</span><span class="nv" style="color: teal;">Std</span><span class="p">;</span></span>
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6
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="perl"></span>
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7
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7
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="o" style="font-weight: 600;">%</span><span class="nv" style="color: teal;">opts</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">();</span></span>
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8
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="perl"><span class="nv" style="color: teal;">getopts</span><span class="p">(</span><span class="s" style="color: #d14;">"2"</span><span class="p">,</span> <span class="o" style="font-weight: 600;">\%</span><span class="nv" style="color: teal;">opts</span><span class="p">);</span></span>
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9
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="perl"><span class="k" style="font-weight: 600;"><span class="idiff left">my</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$is_dbl</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">defined</span></span><span class="p"><span class="idiff">(</span></span><span class="nv" style="color: teal;"><span class="idiff">$opts</span></span><span class="p"><span class="idiff">{</span></span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff right">}</span>);</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="perl"><span class="nv" style="color: teal;">getopts</span><span class="p">(</span><span class="s" style="color: #d14;">"2<span class="idiff left right">f:l:</span>"</span><span class="p">,</span> <span class="o" style="font-weight: 600;">\%</span><span class="nv" style="color: teal;">opts</span><span class="p">);</span></span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="perl"><span class="nb" style="color: #0086b3;"><span class="idiff left">die</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"Usage: mhap2paf.pl [-2] [-f name_list] [-l min_len] <in.mhap>\n"</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">if</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="nv" style="color: teal;"><span class="idiff">@ARGV</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="nv" style="color: teal;"><span class="idiff">t</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff right">STDIN</span></span><span class="p">);</span></span>
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10
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="perl"></span>
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11
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="perl"><span class="nb" style="color: #0086b3;">die</span><span class="p">(</span><span class="s" style="color: #d14;">"Usage: mhap2paf.pl [-2] <in.mhap>\n"</span><span class="p">)</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: teal;">@ARGV</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: teal;">t</span> <span class="bp" style="color: #999;">STDIN</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$is_dbl</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">defined</span><span class="p">(</span><span class="nv" style="color: teal;">$opts</span><span class="p">{</span><span class="mi" style="color: #099;">2</span><span class="p">});</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$min_blen</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">defined</span><span class="p">(</span><span class="nv" style="color: teal;">$opts</span><span class="p">{</span><span class="nv" style="color: teal;">l</span><span class="p">})?</span> <span class="nv" style="color: teal;">$opts</span><span class="p">{</span><span class="nv" style="color: teal;">l</span><span class="p">}</span> <span class="p">:</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">@a</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">();</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="perl"><span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">defined</span> <span class="nv" style="color: teal;">$opts</span><span class="p">{</span><span class="nv" style="color: teal;">f</span><span class="p">})</span> <span class="p">{</span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="nv" style="color: teal;">FH</span><span class="p">,</span> <span class="nv" style="color: teal;">$opts</span><span class="p">{</span><span class="nv" style="color: teal;">f</span><span class="p">}</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">/\.gz$/</span><span class="p">?</span> <span class="s" style="color: #d14;">"gzip -dc $opts{f} |"</span> <span class="p">:</span> <span class="nv" style="color: teal;">$opts</span><span class="p">{</span><span class="nv" style="color: teal;">f</span><span class="p">})</span> <span class="o" style="font-weight: 600;">||</span> <span class="nb" style="color: #0086b3;">die</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="perl"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="o" style="font-weight: 600;"><</span><span class="nv" style="color: teal;">FH</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="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">chomp</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="18" style="width: 35px; color: rgba(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="LC18" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">@t</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">split</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">push</span><span class="p">(</span><span class="nv" style="color: teal;">@a</span><span class="p">,</span> <span class="nv" style="color: teal;">$t</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]);</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="perl"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">close</span><span class="p">(</span><span class="nv" style="color: teal;">FH</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="perl"><span class="p">}</span></span>
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12
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23
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="perl"></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="perl"><span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="o" style="font-weight: 600;"><></span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">chomp</span><span class="p">;</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -18,6 +29,11 @@ while (<>) {</td>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$ml</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="nv" style="color: teal;">$bl</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="nv" style="color: teal;">$r</span> <span class="o" style="font-weight: 600;"><=</span> <span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">.</span><span class="p">?</span> <span class="nv" style="color: teal;">$r</span> <span class="p">:</span> <span class="mf" style="color: #099;">.01</span> <span class="o" style="font-weight: 600;">*</span> <span class="nv" style="color: teal;">$r</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="mf" style="color: #099;">.499</span><span class="p">);</span></span>
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19
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$cm</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"cm:i:"</span> <span class="o" style="font-weight: 600;">.</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="nv" style="color: teal;">$t</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="mf" style="color: #099;">.499</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$rev</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$t</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="nv" style="color: teal;">$t</span><span class="p">[</span><span class="mi" style="color: #099;">8</span><span class="p">]?</span> <span class="s" style="color: #d14;">'+'</span> <span class="p">:</span> <span class="s" style="color: #d14;">'-'</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="perl"> <span class="k" style="font-weight: 600;">next</span> <span class="k" style="font-weight: 600;">if</span> <span class="nv" style="color: teal;">$bl</span> <span class="o" style="font-weight: 600;"><</span> <span class="nv" style="color: teal;">$min_blen</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: teal;">@a</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="perl"> <span class="nv" style="color: teal;">$t</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="nv" style="color: teal;">$a</span><span class="p">[</span><span class="nv" style="color: teal;">$t</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="mi" style="color: #099;">1</span><span class="p">];</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="perl"> <span class="nv" style="color: teal;">$t</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$a</span><span class="p">[</span><span class="nv" style="color: teal;">$t</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">];</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="perl"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="nb" style="color: #0086b3;">join</span><span class="p">(</span><span class="s" style="color: #d14;">"\t"</span><span class="p">,</span> <span class="nv" style="color: teal;">@t</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">7</span><span class="p">,</span><span class="mi" style="color: #099;">5</span><span class="p">,</span><span class="mi" style="color: #099;">6</span><span class="p">],</span> <span class="nv" style="color: teal;">$rev</span><span class="p">,</span> <span class="nv" style="color: teal;">@t</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">,</span><span class="mi" style="color: #099;">11</span><span class="p">,</span><span class="mi" style="color: #099;">9</span><span class="p">,</span><span class="mi" style="color: #099;">10</span><span class="p">],</span> <span class="nv" style="color: teal;">$ml</span><span class="p">,</span> <span class="nv" style="color: teal;">$bl</span><span class="p">,</span> <span class="mi" style="color: #099;">255</span><span class="p">,</span> <span class="nv" style="color: teal;">$cm</span><span class="p">),</span> <span class="s" style="color: #d14;">"\n"</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="nb" style="color: #0086b3;">join</span><span class="p">(</span><span class="s" style="color: #d14;">"\t"</span><span class="p">,</span> <span class="nv" style="color: teal;">@t</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">,</span><span class="mi" style="color: #099;">11</span><span class="p">,</span><span class="mi" style="color: #099;">9</span><span class="p">,</span><span class="mi" style="color: #099;">10</span><span class="p">],</span> <span class="nv" style="color: teal;">$rev</span><span class="p">,</span> <span class="nv" style="color: teal;">@t</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">7</span><span class="p">,</span><span class="mi" style="color: #099;">5</span><span class="p">,</span><span class="mi" style="color: #099;">6</span><span class="p">],</span> <span class="nv" style="color: teal;">$ml</span><span class="p">,</span> <span class="nv" style="color: teal;">$bl</span><span class="p">,</span> <span class="mi" style="color: #099;">255</span><span class="p">,</span> <span class="nv" style="color: teal;">$cm</span><span class="p">),</span> <span class="s" style="color: #d14;">"\n"</span><span class="p">)</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: teal;">$is_dbl</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="perl"><span class="p">}</span></span></pre>
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<a href="https://salsa.debian.org/med-team/miniasm/compare/c23b2121ec3f8082bbb02499edea827181a76fda...d7b6c4f3557ddd7602088589e02ff4ef9e874444#1942408037af3fd9372960c502323746c412a36d"><strong>misc/ov-sen.js</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="javascript"><span class="kd" style="font-weight: 600;">var</span> <span class="nx">getopt</span> <span class="o" style="font-weight: 600;">=</span> <span class="kd" style="font-weight: 600;">function</span><span class="p">(</span><span class="nx">args</span><span class="p">,</span> <span class="nx">ostr</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="javascript"> <span class="kd" style="font-weight: 600;">var</span> <span class="nx">oli</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// option letter list index</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="javascript"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="k" style="font-weight: 600;">typeof</span><span class="p">(</span><span class="nx">getopt</span><span class="p">.</span><span class="nx">place</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="s1" style="color: #d14;">'undefined'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="javascript"> <span class="nx">getopt</span><span class="p">.</span><span class="nx">ind</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="nx">getopt</span><span class="p">.</span><span class="nx">arg</span> <span class="o" style="font-weight: 600;">=</span> <span class="kc" style="font-weight: 600;">null</span><span class="p">,</span> <span class="nx">getopt</span><span class="p">.</span><span class="nx">place</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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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="javascript"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nx">getopt</span><span class="p">.</span><span class="nx">place</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 class="c1" style="color: #998; font-style: italic;">// update scanning pointer</span></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="javascript"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nx">getopt</span><span class="p">.</span><span class="nx">ind</span> <span class="o" style="font-weight: 600;">>=</span> <span class="nx">args</span><span class="p">.</span><span class="nx">length</span> <span class="o" style="font-weight: 600;">||</span> <span class="nx">args</span><span class="p">[</span><span class="nx">getopt</span><span class="p">.</span><span class="nx">ind</span><span class="p">].</span><span class="nx">charAt</span><span class="p">(</span><span class="nx">getopt</span><span class="p">.</span><span class="nx">place</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="s1" style="color: #d14;">'-'</span><span class="p">)</span> <span class="p">{</span></span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="javascript"> <span class="nx">getopt</span><span class="p">.</span><span class="nx">place</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="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="javascript"> <span class="k" style="font-weight: 600;">return</span> <span class="kc" style="font-weight: 600;">null</span><span class="p">;</span></span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="javascript"> <span class="p">}</span></span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="javascript"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nx">getopt</span><span class="p">.</span><span class="nx">place</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;"><</span> <span class="nx">args</span><span class="p">[</span><span class="nx">getopt</span><span class="p">.</span><span class="nx">ind</span><span class="p">].</span><span class="nx">length</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nx">args</span><span class="p">[</span><span class="nx">getopt</span><span class="p">.</span><span class="nx">ind</span><span class="p">].</span><span class="nx">charAt</span><span class="p">(</span><span class="o" style="font-weight: 600;">++</span><span class="nx">getopt</span><span class="p">.</span><span class="nx">place</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="s1" style="color: #d14;">'-'</span><span class="p">)</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">// found "--"</span></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="javascript"> <span class="o" style="font-weight: 600;">++</span><span class="nx">getopt</span><span class="p">.</span><span class="nx">ind</span><span class="p">;</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="javascript"> <span class="nx">getopt</span><span class="p">.</span><span class="nx">place</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="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="javascript"> <span class="k" style="font-weight: 600;">return</span> <span class="kc" style="font-weight: 600;">null</span><span class="p">;</span></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="javascript"> <span class="p">}</span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="javascript"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="javascript"> <span class="kd" style="font-weight: 600;">var</span> <span class="nx">optopt</span> <span class="o" style="font-weight: 600;">=</span> <span class="nx">args</span><span class="p">[</span><span class="nx">getopt</span><span class="p">.</span><span class="nx">ind</span><span class="p">].</span><span class="nx">charAt</span><span class="p">(</span><span class="nx">getopt</span><span class="p">.</span><span class="nx">place</span><span class="o" style="font-weight: 600;">++</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// character checked for validity</span></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="javascript"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nx">optopt</span> <span class="o" style="font-weight: 600;">==</span> <span class="s1" style="color: #d14;">':'</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="nx">oli</span> <span class="o" style="font-weight: 600;">=</span> <span class="nx">ostr</span><span class="p">.</span><span class="nx">indexOf</span><span class="p">(</span><span class="nx">optopt</span><span class="p">))</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="javascript"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nx">optopt</span> <span class="o" style="font-weight: 600;">==</span> <span class="s1" style="color: #d14;">'-'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">return</span> <span class="kc" style="font-weight: 600;">null</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// if the user didn't specify '-' as an option, assume it means null.</span></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="javascript"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nx">getopt</span><span class="p">.</span><span class="nx">place</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="nx">getopt</span><span class="p">.</span><span class="nx">ind</span><span class="p">;</span></span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="javascript"> <span class="k" style="font-weight: 600;">return</span> <span class="s1" style="color: #d14;">'?'</span><span class="p">;</span></span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="javascript"> <span class="p">}</span></span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="javascript"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nx">oli</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">>=</span> <span class="nx">ostr</span><span class="p">.</span><span class="nx">length</span> <span class="o" style="font-weight: 600;">||</span> <span class="nx">ostr</span><span class="p">.</span><span class="nx">charAt</span><span class="p">(</span><span class="o" style="font-weight: 600;">++</span><span class="nx">oli</span><span class="p">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s1" style="color: #d14;">':'</span><span class="p">)</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">// don't need argument</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="javascript"> <span class="nx">getopt</span><span class="p">.</span><span class="nx">arg</span> <span class="o" style="font-weight: 600;">=</span> <span class="kc" style="font-weight: 600;">null</span><span class="p">;</span></span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="javascript"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nx">getopt</span><span class="p">.</span><span class="nx">place</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="nx">getopt</span><span class="p">.</span><span class="nx">place</span> <span class="o" style="font-weight: 600;">>=</span> <span class="nx">args</span><span class="p">[</span><span class="nx">getopt</span><span class="p">.</span><span class="nx">ind</span><span class="p">].</span><span class="nx">length</span><span class="p">)</span> <span class="o" style="font-weight: 600;">++</span><span class="nx">getopt</span><span class="p">.</span><span class="nx">ind</span><span class="p">,</span> <span class="nx">getopt</span><span class="p">.</span><span class="nx">place</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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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="javascript"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">// need an argument</span></span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="javascript"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nx">getopt</span><span class="p">.</span><span class="nx">place</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="nx">getopt</span><span class="p">.</span><span class="nx">place</span> <span class="o" style="font-weight: 600;"><</span> <span class="nx">args</span><span class="p">[</span><span class="nx">getopt</span><span class="p">.</span><span class="nx">ind</span><span class="p">].</span><span class="nx">length</span><span class="p">)</span></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="javascript"> <span class="nx">getopt</span><span class="p">.</span><span class="nx">arg</span> <span class="o" style="font-weight: 600;">=</span> <span class="nx">args</span><span class="p">[</span><span class="nx">getopt</span><span class="p">.</span><span class="nx">ind</span><span class="p">].</span><span class="nx">substr</span><span class="p">(</span><span class="nx">getopt</span><span class="p">.</span><span class="nx">place</span><span class="p">);</span></span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="javascript"> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nx">args</span><span class="p">.</span><span class="nx">length</span> <span class="o" style="font-weight: 600;"><=</span> <span class="o" style="font-weight: 600;">++</span><span class="nx">getopt</span><span class="p">.</span><span class="nx">ind</span><span class="p">)</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">// no arg</span></span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="javascript"> <span class="nx">getopt</span><span class="p">.</span><span class="nx">place</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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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="javascript"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nx">ostr</span><span class="p">.</span><span class="nx">length</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="nx">ostr</span><span class="p">.</span><span class="nx">charAt</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="s1" style="color: #d14;">':'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">return</span> <span class="s1" style="color: #d14;">':'</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="javascript"> <span class="k" style="font-weight: 600;">return</span> <span class="s1" style="color: #d14;">'?'</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="javascript"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="nx">getopt</span><span class="p">.</span><span class="nx">arg</span> <span class="o" style="font-weight: 600;">=</span> <span class="nx">args</span><span class="p">[</span><span class="nx">getopt</span><span class="p">.</span><span class="nx">ind</span><span class="p">];</span> <span class="c1" style="color: #998; font-style: italic;">// white space</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="javascript"> <span class="nx">getopt</span><span class="p">.</span><span class="nx">place</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="LC34" class="line" lang="javascript"> <span class="o" style="font-weight: 600;">++</span><span class="nx">getopt</span><span class="p">.</span><span class="nx">ind</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="javascript"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="javascript"> <span class="k" style="font-weight: 600;">return</span> <span class="nx">optopt</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="javascript"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="javascript"></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="javascript"><span class="kd" style="font-weight: 600;">var</span> <span class="nx">c</span><span class="p">,</span> <span class="nx">min_len</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">2000</span><span class="p">,</span> <span class="nx">min_mapq</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">10</span><span class="p">;</span></span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="javascript"><span class="k" style="font-weight: 600;">while</span> <span class="p">((</span><span class="nx">c</span> <span class="o" style="font-weight: 600;">=</span> <span class="nx">getopt</span><span class="p">(</span><span class="kr" style="font-weight: 600;">arguments</span><span class="p">,</span> <span class="s2" style="color: #d14;">"l:q:"</span><span class="p">))</span> <span class="o" style="font-weight: 600;">!=</span> <span class="kc" style="font-weight: 600;">null</span><span class="p">)</span></span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="javascript"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nx">c</span> <span class="o" style="font-weight: 600;">==</span> <span class="s1" style="color: #d14;">'l'</span><span class="p">)</span> <span class="nx">min_len</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">parseInt</span><span class="p">(</span><span class="nx">getopt</span><span class="p">.</span><span class="nx">arg</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="javascript"> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nx">c</span> <span class="o" style="font-weight: 600;">==</span> <span class="s1" style="color: #d14;">'q'</span><span class="p">)</span> <span class="nx">min_mapq</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">parseInt</span><span class="p">(</span><span class="nx">getopt</span><span class="p">.</span><span class="nx">arg</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="javascript"></span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="javascript"><span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="kr" style="font-weight: 600;">arguments</span><span class="p">.</span><span class="nx">length</span> <span class="o" style="font-weight: 600;">-</span> <span class="nx">getopt</span><span class="p">.</span><span class="nx">ind</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">2</span><span class="p">)</span> <span class="p">{</span></span>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="javascript"> <span class="nx">warn</span><span class="p">(</span><span class="s2" style="color: #d14;">"Usage: k8 ov-sen.js [options] <in.ref-sorted.paf> <in.ovlp.paf>"</span><span class="p">);</span></span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="javascript"> <span class="nx">warn</span><span class="p">(</span><span class="s2" style="color: #d14;">"Options:"</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="javascript"> <span class="nx">warn</span><span class="p">(</span><span class="s2" style="color: #d14;">" -l INT min overlap length [2000]"</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="javascript"> <span class="nx">warn</span><span class="p">(</span><span class="s2" style="color: #d14;">" -q INT min mapping quality [10]"</span><span class="p">);</span></span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="javascript"> <span class="nx">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="javascript"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="javascript"></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="javascript"><span class="kd" style="font-weight: 600;">var</span> <span class="nx">file</span><span class="p">,</span> <span class="nx">buf</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nx">Bytes</span><span class="p">();</span></span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="javascript"></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="javascript"><span class="kd" style="font-weight: 600;">var</span> <span class="nx">h</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{};</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="javascript"></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="javascript"><span class="nx">file</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nx">File</span><span class="p">(</span><span class="kr" style="font-weight: 600;">arguments</span><span class="p">[</span><span class="nx">getopt</span><span class="p">.</span><span class="nx">ind</span><span class="p">]);</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="javascript"><span class="kd" style="font-weight: 600;">var</span> <span class="nx">a</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[];</span></span>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="javascript"><span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="nx">file</span><span class="p">.</span><span class="nx">readline</span><span class="p">(</span><span class="nx">buf</span><span class="p">)</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="javascript"> <span class="kd" style="font-weight: 600;">var</span> <span class="nx">t</span> <span class="o" style="font-weight: 600;">=</span> <span class="nx">buf</span><span class="p">.</span><span class="nx">toString</span><span class="p">().</span><span class="nx">split</span><span class="p">(</span><span class="s2" style="color: #d14;">"</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span><span class="s2" style="color: #d14;">t"</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="javascript"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">parseInt</span><span class="p">(</span><span class="nx">t</span><span class="p">[</span><span class="mi" style="color: #099;">11</span><span class="p">])</span> <span class="o" style="font-weight: 600;"><</span> <span class="nx">min_mapq</span><span class="p">)</span> <span class="k" style="font-weight: 600;">continue</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="javascript"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">parseInt</span><span class="p">(</span><span class="nx">t</span><span class="p">[</span><span class="mi" style="color: #099;">10</span><span class="p">])</span> <span class="o" style="font-weight: 600;"><</span> <span class="nx">min_len</span><span class="p">)</span> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="javascript"> <span class="kd" style="font-weight: 600;">var</span> <span class="nx">st</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">parseInt</span><span class="p">(</span><span class="nx">t</span><span class="p">[</span><span class="mi" style="color: #099;">7</span><span class="p">]),</span> <span class="nx">en</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">parseInt</span><span class="p">(</span><span class="nx">t</span><span class="p">[</span><span class="mi" style="color: #099;">8</span><span class="p">]);</span></span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="javascript"></span>
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<td class="diff-line-num new new_line" data-linenumber="64" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="javascript"> <span class="kd" style="font-weight: 600;">var</span> <span class="nx">n_shift</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="javascript"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nx">a</span><span class="p">.</span><span class="nx">length</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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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="javascript"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kd" style="font-weight: 600;">var</span> <span class="nx">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="nx">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="nx">a</span><span class="p">.</span><span class="nx">length</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="nx">i</span><span class="p">)</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="javascript"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nx">t</span><span class="p">[</span><span class="mi" style="color: #099;">5</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="nx">a</span><span class="p">[</span><span class="nx">i</span><span class="p">][</span><span class="mi" style="color: #099;">1</span><span class="p">])</span> <span class="p">{</span></span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="javascript"> <span class="o" style="font-weight: 600;">++</span><span class="nx">n_shift</span><span class="p">;</span></span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="javascript"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</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="javascript"> <span class="kd" style="font-weight: 600;">var</span> <span class="nx">min_en</span> <span class="o" style="font-weight: 600;">=</span> <span class="nx">a</span><span class="p">[</span><span class="nx">i</span><span class="p">][</span><span class="mi" style="color: #099;">3</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><</span> <span class="nx">en</span><span class="p">?</span> <span class="nx">a</span><span class="p">[</span><span class="nx">i</span><span class="p">][</span><span class="mi" style="color: #099;">3</span><span class="p">]</span> <span class="p">:</span> <span class="nx">en</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="javascript"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nx">min_en</span> <span class="o" style="font-weight: 600;">-</span> <span class="nx">st</span> <span class="o" style="font-weight: 600;">>=</span> <span class="nx">min_len</span><span class="p">)</span> <span class="k" style="font-weight: 600;">break</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="javascript"> <span class="o" style="font-weight: 600;">++</span><span class="nx">n_shift</span><span class="p">;</span></span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="javascript"> <span class="p">}</span></span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="javascript"> <span class="p">}</span></span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="javascript"> <span class="p">}</span></span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="javascript"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nx">n_shift</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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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="javascript"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kd" style="font-weight: 600;">var</span> <span class="nx">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="nx">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="nx">n_shift</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="nx">i</span><span class="p">)</span></span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="javascript"> <span class="nx">a</span><span class="p">.</span><span class="nx">shift</span><span class="p">();</span></span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="javascript"> <span class="p">}</span></span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="javascript"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nx">a</span><span class="p">.</span><span class="nx">length</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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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="javascript"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kd" style="font-weight: 600;">var</span> <span class="nx">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="nx">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="nx">a</span><span class="p">.</span><span class="nx">length</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="nx">i</span><span class="p">)</span> <span class="p">{</span></span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="javascript"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nx">t</span><span class="p">[</span><span class="mi" style="color: #099;">5</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="nx">a</span><span class="p">[</span><span class="nx">i</span><span class="p">][</span><span class="mi" style="color: #099;">1</span><span class="p">])</span> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="javascript"> <span class="kd" style="font-weight: 600;">var</span> <span class="nx">min_en</span> <span class="o" style="font-weight: 600;">=</span> <span class="nx">a</span><span class="p">[</span><span class="nx">i</span><span class="p">][</span><span class="mi" style="color: #099;">3</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><</span> <span class="nx">en</span><span class="p">?</span> <span class="nx">a</span><span class="p">[</span><span class="nx">i</span><span class="p">][</span><span class="mi" style="color: #099;">3</span><span class="p">]</span> <span class="p">:</span> <span class="nx">en</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="84" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="javascript"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nx">min_en</span> <span class="o" style="font-weight: 600;">-</span> <span class="nx">st</span> <span class="o" style="font-weight: 600;"><</span> <span class="nx">min_len</span><span class="p">)</span> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="85" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="javascript"> <span class="nx">h</span><span class="p">[</span><span class="nx">a</span><span class="p">[</span><span class="nx">i</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="s2" style="color: #d14;">"</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span><span class="s2" style="color: #d14;">t"</span> <span class="o" style="font-weight: 600;">+</span> <span class="nx">t</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="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="86" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="javascript"> <span class="c1" style="color: #998; font-style: italic;">//print(a[i][0], t[0], min_en - st);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="87" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="javascript"> <span class="p">}</span></span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="javascript"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="89" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="javascript"> <span class="nx">a</span><span class="p">.</span><span class="nx">push</span><span class="p">([</span><span class="nx">t</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="nx">t</span><span class="p">[</span><span class="mi" style="color: #099;">5</span><span class="p">],</span> <span class="nx">st</span><span class="p">,</span> <span class="nx">en</span><span class="p">]);</span></span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="javascript"><span class="p">}</span></span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="javascript"><span class="nx">file</span><span class="p">.</span><span class="nx">close</span><span class="p">();</span></span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="javascript"></span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="javascript"><span class="nx">file</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nx">File</span><span class="p">(</span><span class="kr" style="font-weight: 600;">arguments</span><span class="p">[</span><span class="nx">getopt</span><span class="p">.</span><span class="nx">ind</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="94" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="javascript"><span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="nx">file</span><span class="p">.</span><span class="nx">readline</span><span class="p">(</span><span class="nx">buf</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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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="javascript"> <span class="kd" style="font-weight: 600;">var</span> <span class="nx">t</span> <span class="o" style="font-weight: 600;">=</span> <span class="nx">buf</span><span class="p">.</span><span class="nx">toString</span><span class="p">().</span><span class="nx">split</span><span class="p">(</span><span class="s2" style="color: #d14;">"</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span><span class="s2" style="color: #d14;">t"</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="javascript"> <span class="kd" style="font-weight: 600;">var</span> <span class="nx">key</span> <span class="o" style="font-weight: 600;">=</span> <span class="nx">t</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="s2" style="color: #d14;">"</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span><span class="s2" style="color: #d14;">t"</span> <span class="o" style="font-weight: 600;">+</span> <span class="nx">t</span><span class="p">[</span><span class="mi" style="color: #099;">5</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="javascript"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nx">h</span><span class="p">[</span><span class="nx">key</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="kc" style="font-weight: 600;">null</span><span class="p">)</span> <span class="o" style="font-weight: 600;">++</span><span class="nx">h</span><span class="p">[</span><span class="nx">key</span><span class="p">];</span></span>
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<td class="diff-line-num new new_line" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="javascript"> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="javascript"> <span class="nx">key</span> <span class="o" style="font-weight: 600;">=</span> <span class="nx">t</span><span class="p">[</span><span class="mi" style="color: #099;">5</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="s2" style="color: #d14;">"</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span><span class="s2" style="color: #d14;">t"</span> <span class="o" style="font-weight: 600;">+</span> <span class="nx">t</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="javascript"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nx">h</span><span class="p">[</span><span class="nx">key</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="kc" style="font-weight: 600;">null</span><span class="p">)</span> <span class="o" style="font-weight: 600;">++</span><span class="nx">h</span><span class="p">[</span><span class="nx">key</span><span class="p">];</span></span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="javascript"> <span class="p">}</span></span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="javascript"><span class="p">}</span></span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="javascript"><span class="nx">file</span><span class="p">.</span><span class="nx">close</span><span class="p">();</span></span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="javascript"></span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="javascript"><span class="nx">buf</span><span class="p">.</span><span class="nx">destroy</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="javascript"></span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="javascript"><span class="kd" style="font-weight: 600;">var</span> <span class="nx">n_ovlp</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="nx">n_missed</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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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="javascript"><span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kd" style="font-weight: 600;">var</span> <span class="nx">key</span> <span class="k" style="font-weight: 600;">in</span> <span class="nx">h</span><span class="p">)</span> <span class="p">{</span></span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="javascript"> <span class="o" style="font-weight: 600;">++</span><span class="nx">n_ovlp</span><span class="p">;</span></span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="javascript"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nx">h</span><span class="p">[</span><span class="nx">key</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="o" style="font-weight: 600;">++</span><span class="nx">n_missed</span><span class="p">;</span></span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="javascript"><span class="p">}</span></span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="javascript"><span class="nx">print</span><span class="p">(</span><span class="nx">n_ovlp</span> <span class="o" style="font-weight: 600;">+</span> <span class="s2" style="color: #d14;">" overlaps"</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="113" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="javascript"><span class="nx">print</span><span class="p">(</span><span class="nx">n_missed</span> <span class="o" style="font-weight: 600;">+</span> <span class="s2" style="color: #d14;">" missed"</span><span class="p">);</span></span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="javascript"><span class="nx">print</span><span class="p">((</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">-</span> <span class="nx">n_missed</span><span class="o" style="font-weight: 600;">/</span><span class="nx">n_ovlp</span><span class="p">).</span><span class="nx">toFixed</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="s2" style="color: #d14;">" sensitivity"</span><span class="p">);</span></span></pre>
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<li id="900271b74f3c1bc24ab7b5dae82089fe297cedde">
<a href="https://salsa.debian.org/med-team/miniasm/compare/c23b2121ec3f8082bbb02499edea827181a76fda...d7b6c4f3557ddd7602088589e02ff4ef9e874444#900271b74f3c1bc24ab7b5dae82089fe297cedde"><strong>misc/paftop.js</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="javascript"><span class="kd" style="font-weight: 600;">var</span> <span class="nx">getopt</span> <span class="o" style="font-weight: 600;">=</span> <span class="kd" style="font-weight: 600;">function</span><span class="p">(</span><span class="nx">args</span><span class="p">,</span> <span class="nx">ostr</span><span class="p">)</span> <span class="p">{</span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="javascript"> <span class="kd" style="font-weight: 600;">var</span> <span class="nx">oli</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// option letter list index</span></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="javascript"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="k" style="font-weight: 600;">typeof</span><span class="p">(</span><span class="nx">getopt</span><span class="p">.</span><span class="nx">place</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="s1" style="color: #d14;">'undefined'</span><span class="p">)</span></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="javascript"> <span class="nx">getopt</span><span class="p">.</span><span class="nx">ind</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="nx">getopt</span><span class="p">.</span><span class="nx">arg</span> <span class="o" style="font-weight: 600;">=</span> <span class="kc" style="font-weight: 600;">null</span><span class="p">,</span> <span class="nx">getopt</span><span class="p">.</span><span class="nx">place</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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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="javascript"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nx">getopt</span><span class="p">.</span><span class="nx">place</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 class="c1" style="color: #998; font-style: italic;">// update scanning pointer</span></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="javascript"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nx">getopt</span><span class="p">.</span><span class="nx">ind</span> <span class="o" style="font-weight: 600;">>=</span> <span class="nx">args</span><span class="p">.</span><span class="nx">length</span> <span class="o" style="font-weight: 600;">||</span> <span class="nx">args</span><span class="p">[</span><span class="nx">getopt</span><span class="p">.</span><span class="nx">ind</span><span class="p">].</span><span class="nx">charAt</span><span class="p">(</span><span class="nx">getopt</span><span class="p">.</span><span class="nx">place</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="s1" style="color: #d14;">'-'</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="javascript"> <span class="nx">getopt</span><span class="p">.</span><span class="nx">place</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="LC8" class="line" lang="javascript"> <span class="k" style="font-weight: 600;">return</span> <span class="kc" style="font-weight: 600;">null</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="javascript"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="javascript"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nx">getopt</span><span class="p">.</span><span class="nx">place</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;"><</span> <span class="nx">args</span><span class="p">[</span><span class="nx">getopt</span><span class="p">.</span><span class="nx">ind</span><span class="p">].</span><span class="nx">length</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nx">args</span><span class="p">[</span><span class="nx">getopt</span><span class="p">.</span><span class="nx">ind</span><span class="p">].</span><span class="nx">charAt</span><span class="p">(</span><span class="o" style="font-weight: 600;">++</span><span class="nx">getopt</span><span class="p">.</span><span class="nx">place</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="s1" style="color: #d14;">'-'</span><span class="p">)</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">// found "--"</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="javascript"> <span class="o" style="font-weight: 600;">++</span><span class="nx">getopt</span><span class="p">.</span><span class="nx">ind</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="javascript"> <span class="nx">getopt</span><span class="p">.</span><span class="nx">place</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="LC13" class="line" lang="javascript"> <span class="k" style="font-weight: 600;">return</span> <span class="kc" style="font-weight: 600;">null</span><span class="p">;</span></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="javascript"> <span class="p">}</span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="javascript"> <span class="p">}</span></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="javascript"> <span class="kd" style="font-weight: 600;">var</span> <span class="nx">optopt</span> <span class="o" style="font-weight: 600;">=</span> <span class="nx">args</span><span class="p">[</span><span class="nx">getopt</span><span class="p">.</span><span class="nx">ind</span><span class="p">].</span><span class="nx">charAt</span><span class="p">(</span><span class="nx">getopt</span><span class="p">.</span><span class="nx">place</span><span class="o" style="font-weight: 600;">++</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// character checked for validity</span></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="javascript"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nx">optopt</span> <span class="o" style="font-weight: 600;">==</span> <span class="s1" style="color: #d14;">':'</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="nx">oli</span> <span class="o" style="font-weight: 600;">=</span> <span class="nx">ostr</span><span class="p">.</span><span class="nx">indexOf</span><span class="p">(</span><span class="nx">optopt</span><span class="p">))</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="javascript"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nx">optopt</span> <span class="o" style="font-weight: 600;">==</span> <span class="s1" style="color: #d14;">'-'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">return</span> <span class="kc" style="font-weight: 600;">null</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// if the user didn't specify '-' as an option, assume it means null.</span></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="javascript"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nx">getopt</span><span class="p">.</span><span class="nx">place</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="nx">getopt</span><span class="p">.</span><span class="nx">ind</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="javascript"> <span class="k" style="font-weight: 600;">return</span> <span class="s1" style="color: #d14;">'?'</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="javascript"> <span class="p">}</span></span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="javascript"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nx">oli</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">>=</span> <span class="nx">ostr</span><span class="p">.</span><span class="nx">length</span> <span class="o" style="font-weight: 600;">||</span> <span class="nx">ostr</span><span class="p">.</span><span class="nx">charAt</span><span class="p">(</span><span class="o" style="font-weight: 600;">++</span><span class="nx">oli</span><span class="p">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s1" style="color: #d14;">':'</span><span class="p">)</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">// don't need argument</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="javascript"> <span class="nx">getopt</span><span class="p">.</span><span class="nx">arg</span> <span class="o" style="font-weight: 600;">=</span> <span class="kc" style="font-weight: 600;">null</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="javascript"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nx">getopt</span><span class="p">.</span><span class="nx">place</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="nx">getopt</span><span class="p">.</span><span class="nx">place</span> <span class="o" style="font-weight: 600;">>=</span> <span class="nx">args</span><span class="p">[</span><span class="nx">getopt</span><span class="p">.</span><span class="nx">ind</span><span class="p">].</span><span class="nx">length</span><span class="p">)</span> <span class="o" style="font-weight: 600;">++</span><span class="nx">getopt</span><span class="p">.</span><span class="nx">ind</span><span class="p">,</span> <span class="nx">getopt</span><span class="p">.</span><span class="nx">place</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="LC25" class="line" lang="javascript"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">// need an argument</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="javascript"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nx">getopt</span><span class="p">.</span><span class="nx">place</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="nx">getopt</span><span class="p">.</span><span class="nx">place</span> <span class="o" style="font-weight: 600;"><</span> <span class="nx">args</span><span class="p">[</span><span class="nx">getopt</span><span class="p">.</span><span class="nx">ind</span><span class="p">].</span><span class="nx">length</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="javascript"> <span class="nx">getopt</span><span class="p">.</span><span class="nx">arg</span> <span class="o" style="font-weight: 600;">=</span> <span class="nx">args</span><span class="p">[</span><span class="nx">getopt</span><span class="p">.</span><span class="nx">ind</span><span class="p">].</span><span class="nx">substr</span><span class="p">(</span><span class="nx">getopt</span><span class="p">.</span><span class="nx">place</span><span class="p">);</span></span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="javascript"> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nx">args</span><span class="p">.</span><span class="nx">length</span> <span class="o" style="font-weight: 600;"><=</span> <span class="o" style="font-weight: 600;">++</span><span class="nx">getopt</span><span class="p">.</span><span class="nx">ind</span><span class="p">)</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">// no arg</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="javascript"> <span class="nx">getopt</span><span class="p">.</span><span class="nx">place</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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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="javascript"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nx">ostr</span><span class="p">.</span><span class="nx">length</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="nx">ostr</span><span class="p">.</span><span class="nx">charAt</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="s1" style="color: #d14;">':'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">return</span> <span class="s1" style="color: #d14;">':'</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="javascript"> <span class="k" style="font-weight: 600;">return</span> <span class="s1" style="color: #d14;">'?'</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="javascript"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="nx">getopt</span><span class="p">.</span><span class="nx">arg</span> <span class="o" style="font-weight: 600;">=</span> <span class="nx">args</span><span class="p">[</span><span class="nx">getopt</span><span class="p">.</span><span class="nx">ind</span><span class="p">];</span> <span class="c1" style="color: #998; font-style: italic;">// white space</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="javascript"> <span class="nx">getopt</span><span class="p">.</span><span class="nx">place</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="LC34" class="line" lang="javascript"> <span class="o" style="font-weight: 600;">++</span><span class="nx">getopt</span><span class="p">.</span><span class="nx">ind</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="javascript"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="javascript"> <span class="k" style="font-weight: 600;">return</span> <span class="nx">optopt</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="javascript"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="javascript"></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="javascript"><span class="kd" style="font-weight: 600;">function</span> <span class="nx">pafmask</span><span class="p">(</span><span class="nx">a</span><span class="p">,</span> <span class="nx">mask_level</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="javascript"><span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="javascript"> <span class="kd" style="font-weight: 600;">var</span> <span class="nx">k</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="LC42" class="line" lang="javascript"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kd" style="font-weight: 600;">var</span> <span class="nx">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="nx">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="nx">a</span><span class="p">.</span><span class="nx">length</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="nx">i</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="javascript"> <span class="kd" style="font-weight: 600;">var</span> <span class="nx">j</span><span class="p">,</span> <span class="nx">ai</span> <span class="o" style="font-weight: 600;">=</span> <span class="nx">a</span><span class="p">[</span><span class="nx">i</span><span class="p">];</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="javascript"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="nx">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="nx">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="nx">k</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="nx">j</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="javascript"> <span class="kd" style="font-weight: 600;">var</span> <span class="nx">ol</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="nx">aj</span> <span class="o" style="font-weight: 600;">=</span> <span class="nx">a</span><span class="p">[</span><span class="nx">j</span><span class="p">];</span></span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="javascript"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nx">ai</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="nx">aj</span><span class="p">[</span><span class="mi" style="color: #099;">2</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="javascript"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nx">ai</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]</span> <span class="o" style="font-weight: 600;">></span> <span class="nx">aj</span><span class="p">[</span><span class="mi" style="color: #099;">2</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="javascript"> <span class="nx">ol</span> <span class="o" style="font-weight: 600;">=</span> <span class="nx">ai</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="nx">aj</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">];</span></span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="javascript"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="javascript"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nx">aj</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]</span> <span class="o" style="font-weight: 600;">></span> <span class="nx">ai</span><span class="p">[</span><span class="mi" style="color: #099;">2</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="javascript"> <span class="nx">ol</span> <span class="o" style="font-weight: 600;">=</span> <span class="nx">aj</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="nx">ai</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">];</span></span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="javascript"> <span class="p">}</span></span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="javascript"> <span class="kd" style="font-weight: 600;">var</span> <span class="nx">min_l</span> <span class="o" style="font-weight: 600;">=</span> <span class="nx">ai</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="nx">ai</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="nx">aj</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="nx">aj</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]?</span> <span class="nx">ai</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="nx">ai</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="p">:</span> <span class="nx">aj</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="nx">aj</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">];</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="javascript"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nx">ol</span> <span class="o" style="font-weight: 600;">></span> <span class="nx">min_l</span> <span class="o" style="font-weight: 600;">*</span> <span class="nx">mask_level</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="javascript"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="javascript"> <span class="p">}</span></span>
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="javascript"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nx">j</span> <span class="o" style="font-weight: 600;">==</span> <span class="nx">k</span><span class="p">)</span> <span class="nx">a</span><span class="p">[</span><span class="nx">k</span><span class="o" style="font-weight: 600;">++</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="nx">ai</span><span class="p">;</span></span>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="javascript"> <span class="p">}</span></span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="javascript"> <span class="nx">a</span><span class="p">.</span><span class="nx">length</span> <span class="o" style="font-weight: 600;">=</span> <span class="nx">k</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="javascript"><span class="p">}</span></span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="javascript"></span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="javascript"><span class="kd" style="font-weight: 600;">function</span> <span class="nx">pafmerge</span><span class="p">(</span><span class="nx">a</span><span class="p">,</span> <span class="nx">max_gap</span><span class="p">)</span></span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="javascript"><span class="p">{</span></span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="javascript"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kd" style="font-weight: 600;">var</span> <span class="nx">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="nx">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="nx">a</span><span class="p">.</span><span class="nx">length</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="nx">i</span><span class="p">)</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="javascript"> <span class="kd" style="font-weight: 600;">var</span> <span class="nx">ai</span> <span class="o" style="font-weight: 600;">=</span> <span class="nx">a</span><span class="p">[</span><span class="nx">i</span><span class="p">];</span></span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="javascript"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kd" style="font-weight: 600;">var</span> <span class="nx">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="nx">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="nx">i</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="nx">j</span><span class="p">)</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="javascript"> <span class="kd" style="font-weight: 600;">var</span> <span class="nx">aj</span> <span class="o" style="font-weight: 600;">=</span> <span class="nx">a</span><span class="p">[</span><span class="nx">j</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="javascript"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nx">aj</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="nx">ai</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="nx">aj</span><span class="p">[</span><span class="mi" style="color: #099;">5</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="nx">ai</span><span class="p">[</span><span class="mi" style="color: #099;">5</span><span class="p">])</span> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// diff strand or chr</span></span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="javascript"> <span class="kd" style="font-weight: 600;">var</span> <span class="nx">ts</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="nx">ai</span><span class="p">[</span><span class="mi" style="color: #099;">7</span><span class="p">],</span> <span class="nx">aj</span><span class="p">[</span><span class="mi" style="color: #099;">7</span><span class="p">]],</span> <span class="nx">te</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="nx">ai</span><span class="p">[</span><span class="mi" style="color: #099;">8</span><span class="p">],</span> <span class="nx">aj</span><span class="p">[</span><span class="mi" style="color: #099;">8</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="javascript"> <span class="kd" style="font-weight: 600;">var</span> <span class="nx">qs</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="nx">ai</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">],</span> <span class="nx">aj</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]],</span> <span class="nx">qe</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="nx">ai</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">],</span> <span class="nx">aj</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]];</span></span>
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<td class="diff-line-num new new_line" data-linenumber="71" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="javascript"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nx">qs</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="nx">qs</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">])</span> <span class="p">{</span></span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="javascript"> <span class="nx">qs</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="nx">aj</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">],</span> <span class="nx">ai</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]],</span> <span class="nx">qe</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="nx">aj</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">],</span> <span class="nx">ai</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]];</span></span>
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<td class="diff-line-num new new_line" data-linenumber="73" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="javascript"> <span class="nx">ts</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="nx">aj</span><span class="p">[</span><span class="mi" style="color: #099;">7</span><span class="p">],</span> <span class="nx">ai</span><span class="p">[</span><span class="mi" style="color: #099;">7</span><span class="p">]],</span> <span class="nx">te</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="nx">aj</span><span class="p">[</span><span class="mi" style="color: #099;">8</span><span class="p">],</span> <span class="nx">ai</span><span class="p">[</span><span class="mi" style="color: #099;">8</span><span class="p">]];</span></span>
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<td class="diff-line-num new new_line" data-linenumber="74" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="javascript"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nx">ai</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="s1" style="color: #d14;">'-'</span><span class="p">)</span> <span class="p">{</span></span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="javascript"> <span class="nx">ts</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="nx">aj</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="nx">aj</span><span class="p">[</span><span class="mi" style="color: #099;">8</span><span class="p">],</span> <span class="nx">ai</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="nx">ai</span><span class="p">[</span><span class="mi" style="color: #099;">8</span><span class="p">]];</span></span>
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<td class="diff-line-num new new_line" data-linenumber="76" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="javascript"> <span class="nx">te</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="nx">aj</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="nx">aj</span><span class="p">[</span><span class="mi" style="color: #099;">7</span><span class="p">],</span> <span class="nx">ai</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="nx">ai</span><span class="p">[</span><span class="mi" style="color: #099;">7</span><span class="p">]];</span></span>
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<td class="diff-line-num new new_line" data-linenumber="77" style="width: 35px; color: rgba(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="LC77" class="line" lang="javascript"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="78" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="javascript"> <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="79" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="javascript"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nx">ai</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="s1" style="color: #d14;">'-'</span><span class="p">)</span> <span class="p">{</span></span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="javascript"> <span class="nx">ts</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="nx">ai</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="nx">ai</span><span class="p">[</span><span class="mi" style="color: #099;">8</span><span class="p">],</span> <span class="nx">aj</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="nx">aj</span><span class="p">[</span><span class="mi" style="color: #099;">8</span><span class="p">]];</span></span>
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<td class="diff-line-num new new_line" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="javascript"> <span class="nx">te</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="nx">ai</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="nx">ai</span><span class="p">[</span><span class="mi" style="color: #099;">7</span><span class="p">],</span> <span class="nx">aj</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="nx">aj</span><span class="p">[</span><span class="mi" style="color: #099;">7</span><span class="p">]];</span></span>
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="javascript"> <span class="p">}</span></span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="javascript"> <span class="p">}</span></span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="javascript"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nx">qe</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="nx">qe</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">])</span> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// contained</span></span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="javascript"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nx">ts</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="nx">ts</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">])</span> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="86" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="javascript"> <span class="kd" style="font-weight: 600;">var</span> <span class="nx">qg</span> <span class="o" style="font-weight: 600;">=</span> <span class="nx">qs</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="nx">qe</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="nx">tg</span> <span class="o" style="font-weight: 600;">=</span> <span class="nx">ts</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="nx">te</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></span>
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<td class="diff-line-num new new_line" data-linenumber="87" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="javascript"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="nx">qg</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="nx">tg</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="nb" style="color: #0086b3;">Math</span><span class="p">.</span><span class="nx">abs</span><span class="p">(</span><span class="nx">tg</span> <span class="o" style="font-weight: 600;">-</span> <span class="nx">qg</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><</span> <span class="nx">max_gap</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="88" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="javascript"> <span class="c1" style="color: #998; font-style: italic;">//print("Merged: ["+ai[2]+","+ai[3]+") <=> ["+aj[2]+","+aj[3]+") "+ai[4]+" ["+ai[7]+","+ai[8]+") <=> ["+aj[7]+","+aj[8]+")");</span></span>
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<td class="diff-line-num new new_line" data-linenumber="89" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="javascript"> <span class="nx">aj</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="nx">qs</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="nx">aj</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="nx">qe</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">];</span></span>
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<td class="diff-line-num new new_line" data-linenumber="90" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="javascript"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nx">aj</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="s1" style="color: #d14;">'+'</span><span class="p">)</span> <span class="p">{</span></span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="javascript"> <span class="nx">aj</span><span class="p">[</span><span class="mi" style="color: #099;">7</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="nx">ts</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="nx">aj</span><span class="p">[</span><span class="mi" style="color: #099;">8</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="nx">te</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">];</span></span>
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<td class="diff-line-num new new_line" data-linenumber="92" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="javascript"> <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="93" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="javascript"> <span class="nx">aj</span><span class="p">[</span><span class="mi" style="color: #099;">7</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="nx">aj</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="nx">te</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">],</span> <span class="nx">aj</span><span class="p">[</span><span class="mi" style="color: #099;">8</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="nx">aj</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="nx">ts</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></span>
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<td class="diff-line-num new new_line" data-linenumber="94" style="width: 35px; color: rgba(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="LC94" class="line" lang="javascript"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="95" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="javascript"> <span class="nx">aj</span><span class="p">[</span><span class="mi" style="color: #099;">9</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="nx">ai</span><span class="p">[</span><span class="mi" style="color: #099;">9</span><span class="p">],</span> <span class="nx">aj</span><span class="p">[</span><span class="mi" style="color: #099;">10</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="nx">ai</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="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="javascript"> <span class="nx">aj</span><span class="p">[</span><span class="mi" style="color: #099;">11</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="nx">aj</span><span class="p">[</span><span class="mi" style="color: #099;">11</span><span class="p">]</span> <span class="o" style="font-weight: 600;">></span> <span class="nx">ai</span><span class="p">[</span><span class="mi" style="color: #099;">11</span><span class="p">]?</span> <span class="nx">aj</span><span class="p">[</span><span class="mi" style="color: #099;">11</span><span class="p">]</span> <span class="p">:</span> <span class="nx">ai</span><span class="p">[</span><span class="mi" style="color: #099;">11</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="javascript"> <span class="nx">a</span><span class="p">[</span><span class="nx">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</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="javascript"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="javascript"> <span class="p">}</span></span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="javascript"> <span class="p">}</span></span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="javascript"> <span class="p">}</span></span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="javascript"> <span class="kd" style="font-weight: 600;">var</span> <span class="nx">k</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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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="javascript"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kd" style="font-weight: 600;">var</span> <span class="nx">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="nx">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="nx">a</span><span class="p">.</span><span class="nx">length</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="nx">i</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="javascript"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nx">a</span><span class="p">[</span><span class="nx">i</span><span class="p">].</span><span class="nx">length</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="nx">a</span><span class="p">[</span><span class="nx">k</span><span class="o" style="font-weight: 600;">++</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="nx">a</span><span class="p">[</span><span class="nx">i</span><span class="p">];</span></span>
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<td class="diff-line-num new new_line" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="javascript"> <span class="nx">a</span><span class="p">.</span><span class="nx">length</span> <span class="o" style="font-weight: 600;">=</span> <span class="nx">k</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="javascript"><span class="p">}</span></span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="javascript"></span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="javascript"><span class="kd" style="font-weight: 600;">function</span> <span class="nx">paftop</span><span class="p">(</span><span class="nx">a</span><span class="p">,</span> <span class="nx">mask_level</span><span class="p">,</span> <span class="nx">max_gap</span><span class="p">)</span></span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="javascript"><span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="javascript"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kd" style="font-weight: 600;">var</span> <span class="nx">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="nx">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="nx">a</span><span class="p">.</span><span class="nx">length</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="nx">i</span><span class="p">)</span> <span class="p">{</span></span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="javascript"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kd" style="font-weight: 600;">var</span> <span class="nx">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="nx">j</span> <span class="o" style="font-weight: 600;"><=</span> <span class="mi" style="color: #099;">3</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="nx">j</span><span class="p">)</span> <span class="nx">a</span><span class="p">[</span><span class="nx">i</span><span class="p">][</span><span class="nx">j</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">parseInt</span><span class="p">(</span><span class="nx">a</span><span class="p">[</span><span class="nx">i</span><span class="p">][</span><span class="nx">j</span><span class="p">]);</span></span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="javascript"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kd" style="font-weight: 600;">var</span> <span class="nx">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">6</span><span class="p">;</span> <span class="nx">j</span> <span class="o" style="font-weight: 600;"><=</span> <span class="mi" style="color: #099;">11</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="nx">j</span><span class="p">)</span> <span class="nx">a</span><span class="p">[</span><span class="nx">i</span><span class="p">][</span><span class="nx">j</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">parseInt</span><span class="p">(</span><span class="nx">a</span><span class="p">[</span><span class="nx">i</span><span class="p">][</span><span class="nx">j</span><span class="p">]);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="113" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="javascript"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="114" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="javascript"> <span class="nx">a</span><span class="p">.</span><span class="nx">sort</span><span class="p">(</span><span class="kd" style="font-weight: 600;">function</span><span class="p">(</span><span class="nx">x</span><span class="p">,</span><span class="nx">y</span><span class="p">){</span><span class="k" style="font-weight: 600;">return</span> <span class="nx">y</span><span class="p">[</span><span class="mi" style="color: #099;">9</span><span class="p">]</span><span class="o" style="font-weight: 600;">-</span><span class="nx">x</span><span class="p">[</span><span class="mi" style="color: #099;">9</span><span class="p">];});</span></span>
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<td class="diff-line-num new new_line" data-linenumber="115" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="javascript"> <span class="nx">pafmask</span><span class="p">(</span><span class="nx">a</span><span class="p">,</span> <span class="nx">mask_level</span><span class="p">);</span></span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="javascript"> <span class="nx">pafmerge</span><span class="p">(</span><span class="nx">a</span><span class="p">,</span> <span class="nx">max_gap</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">
117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="javascript"> <span class="nx">pafmask</span><span class="p">(</span><span class="nx">a</span><span class="p">,</span> <span class="nx">mask_level</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="javascript"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kd" style="font-weight: 600;">var</span> <span class="nx">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="nx">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="nx">a</span><span class="p">.</span><span class="nx">length</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="nx">i</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="javascript"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nx">a</span><span class="p">[</span><span class="nx">i</span><span class="p">].</span><span class="nx">length</span><span class="p">)</span> <span class="nx">print</span><span class="p">(</span><span class="nx">a</span><span class="p">[</span><span class="nx">i</span><span class="p">].</span><span class="nx">join</span><span class="p">(</span><span class="s2" style="color: #d14;">"</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span><span class="s2" style="color: #d14;">t"</span><span class="p">));</span></span>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="javascript"><span class="p">}</span></span>
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="javascript"></span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="javascript"><span class="kd" style="font-weight: 600;">var</span> <span class="nx">c</span><span class="p">,</span> <span class="nx">mask_level</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">.</span><span class="mi" style="color: #099;">5</span><span class="p">,</span> <span class="nx">max_gap</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1000</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="123" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="javascript"><span class="k" style="font-weight: 600;">while</span> <span class="p">((</span><span class="nx">c</span> <span class="o" style="font-weight: 600;">=</span> <span class="nx">getopt</span><span class="p">(</span><span class="kr" style="font-weight: 600;">arguments</span><span class="p">,</span> <span class="s1" style="color: #d14;">'m:g:'</span><span class="p">))</span> <span class="o" style="font-weight: 600;">!=</span> <span class="kc" style="font-weight: 600;">null</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="124" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="javascript"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nx">c</span> <span class="o" style="font-weight: 600;">==</span> <span class="s1" style="color: #d14;">'m'</span><span class="p">)</span> <span class="nx">mask_level</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">parseFloat</span><span class="p">(</span><span class="nx">getopt</span><span class="p">.</span><span class="nx">arg</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="125" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="javascript"> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nx">c</span> <span class="o" style="font-weight: 600;">==</span> <span class="s1" style="color: #d14;">'g'</span><span class="p">)</span> <span class="nx">max_gap</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">parseInt</span><span class="p">(</span><span class="nx">getopt</span><span class="p">.</span><span class="nx">arg</span><span class="p">);</span></span>
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126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="javascript"></span>
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127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="javascript"><span class="kd" style="font-weight: 600;">var</span> <span class="nx">file</span> <span class="o" style="font-weight: 600;">=</span> <span class="kr" style="font-weight: 600;">arguments</span><span class="p">.</span><span class="nx">length</span> <span class="o" style="font-weight: 600;">==</span> <span class="nx">getopt</span><span class="p">.</span><span class="nx">ind</span><span class="p">?</span> <span class="k" style="font-weight: 600;">new</span> <span class="nx">File</span><span class="p">()</span> <span class="p">:</span> <span class="k" style="font-weight: 600;">new</span> <span class="nx">File</span><span class="p">(</span><span class="kr" style="font-weight: 600;">arguments</span><span class="p">[</span><span class="nx">getopt</span><span class="p">.</span><span class="nx">ind</span><span class="p">]);</span></span>
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128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="javascript"><span class="kd" style="font-weight: 600;">var</span> <span class="nx">buf</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nx">Bytes</span><span class="p">();</span></span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="javascript"></span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="javascript"><span class="kd" style="font-weight: 600;">var</span> <span class="nx">last</span> <span class="o" style="font-weight: 600;">=</span> <span class="kc" style="font-weight: 600;">null</span><span class="p">,</span> <span class="nx">a</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[];</span></span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="javascript"><span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="nx">file</span><span class="p">.</span><span class="nx">readline</span><span class="p">(</span><span class="nx">buf</span><span class="p">)</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="javascript"> <span class="kd" style="font-weight: 600;">var</span> <span class="nx">t</span> <span class="o" style="font-weight: 600;">=</span> <span class="nx">buf</span><span class="p">.</span><span class="nx">toString</span><span class="p">().</span><span class="nx">split</span><span class="p">(</span><span class="s2" style="color: #d14;">"</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span><span class="s2" style="color: #d14;">t"</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="133" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="javascript"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nx">t</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="nx">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="134" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="javascript"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nx">a</span><span class="p">.</span><span class="nx">length</span><span class="p">)</span> <span class="nx">paftop</span><span class="p">(</span><span class="nx">a</span><span class="p">,</span> <span class="nx">mask_level</span><span class="p">,</span> <span class="nx">max_gap</span><span class="p">);</span></span>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="javascript"> <span class="nx">a</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[],</span> <span class="nx">last</span> <span class="o" style="font-weight: 600;">=</span> <span class="nx">t</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="javascript"> <span class="p">}</span></span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="javascript"> <span class="nx">a</span><span class="p">.</span><span class="nx">push</span><span class="p">(</span><span class="nx">t</span><span class="p">);</span></span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="javascript"><span class="p">}</span></span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="javascript"><span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nx">a</span><span class="p">.</span><span class="nx">length</span><span class="p">)</span> <span class="nx">paftop</span><span class="p">(</span><span class="nx">a</span><span class="p">,</span> <span class="nx">mask_level</span><span class="p">,</span> <span class="nx">max_gap</span><span class="p">);</span></span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="javascript"></span>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="javascript"><span class="nx">buf</span><span class="p">.</span><span class="nx">destroy</span><span class="p">();</span></span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="javascript"><span class="nx">file</span><span class="p">.</span><span class="nx">close</span><span class="p">();</span></span></pre>
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<a href="https://salsa.debian.org/med-team/miniasm/compare/c23b2121ec3f8082bbb02499edea827181a76fda...d7b6c4f3557ddd7602088589e02ff4ef9e874444#54c16df25fed2df36be836f971ed39d117781c0d"><strong>misc/sam2paf.js</strong></a>
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1
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="javascript"><span class="kd" style="font-weight: 600;">var</span> <span class="nx">file</span> <span class="o" style="font-weight: 600;">=</span> <span class="kr" style="font-weight: 600;">arguments</span><span class="p">.</span><span class="nx">length</span><span class="p">?</span> <span class="k" style="font-weight: 600;">new</span> <span class="nx">File</span><span class="p">(</span><span class="kr" style="font-weight: 600;">arguments</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span> <span class="p">:</span> <span class="k" style="font-weight: 600;">new</span> <span class="nx">File</span><span class="p">();</span></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="javascript"><span class="kd" style="font-weight: 600;">var</span> <span class="nx">getopt</span> <span class="o" style="font-weight: 600;">=</span> <span class="kd" style="font-weight: 600;">function</span><span class="p">(</span><span class="nx">args</span><span class="p">,</span> <span class="nx">ostr</span><span class="p">)</span> <span class="p">{</span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="javascript"> <span class="kd" style="font-weight: 600;">var</span> <span class="nx">oli</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// option letter list index</span></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="javascript"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="k" style="font-weight: 600;">typeof</span><span class="p">(</span><span class="nx">getopt</span><span class="p">.</span><span class="nx">place</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="s1" style="color: #d14;">'undefined'</span><span class="p">)</span></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="javascript"> <span class="nx">getopt</span><span class="p">.</span><span class="nx">ind</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="nx">getopt</span><span class="p">.</span><span class="nx">arg</span> <span class="o" style="font-weight: 600;">=</span> <span class="kc" style="font-weight: 600;">null</span><span class="p">,</span> <span class="nx">getopt</span><span class="p">.</span><span class="nx">place</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="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="javascript"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nx">getopt</span><span class="p">.</span><span class="nx">place</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 class="c1" style="color: #998; font-style: italic;">// update scanning pointer</span></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="javascript"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nx">getopt</span><span class="p">.</span><span class="nx">ind</span> <span class="o" style="font-weight: 600;">>=</span> <span class="nx">args</span><span class="p">.</span><span class="nx">length</span> <span class="o" style="font-weight: 600;">||</span> <span class="nx">args</span><span class="p">[</span><span class="nx">getopt</span><span class="p">.</span><span class="nx">ind</span><span class="p">].</span><span class="nx">charAt</span><span class="p">(</span><span class="nx">getopt</span><span class="p">.</span><span class="nx">place</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="s1" style="color: #d14;">'-'</span><span class="p">)</span> <span class="p">{</span></span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="javascript"> <span class="nx">getopt</span><span class="p">.</span><span class="nx">place</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="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="javascript"> <span class="k" style="font-weight: 600;">return</span> <span class="kc" style="font-weight: 600;">null</span><span class="p">;</span></span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="javascript"> <span class="p">}</span></span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="javascript"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nx">getopt</span><span class="p">.</span><span class="nx">place</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;"><</span> <span class="nx">args</span><span class="p">[</span><span class="nx">getopt</span><span class="p">.</span><span class="nx">ind</span><span class="p">].</span><span class="nx">length</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nx">args</span><span class="p">[</span><span class="nx">getopt</span><span class="p">.</span><span class="nx">ind</span><span class="p">].</span><span class="nx">charAt</span><span class="p">(</span><span class="o" style="font-weight: 600;">++</span><span class="nx">getopt</span><span class="p">.</span><span class="nx">place</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="s1" style="color: #d14;">'-'</span><span class="p">)</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">// found "--"</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="javascript"> <span class="o" style="font-weight: 600;">++</span><span class="nx">getopt</span><span class="p">.</span><span class="nx">ind</span><span class="p">;</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="javascript"> <span class="nx">getopt</span><span class="p">.</span><span class="nx">place</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="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="javascript"> <span class="k" style="font-weight: 600;">return</span> <span class="kc" style="font-weight: 600;">null</span><span class="p">;</span></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="javascript"> <span class="p">}</span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="javascript"> <span class="p">}</span></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="javascript"> <span class="kd" style="font-weight: 600;">var</span> <span class="nx">optopt</span> <span class="o" style="font-weight: 600;">=</span> <span class="nx">args</span><span class="p">[</span><span class="nx">getopt</span><span class="p">.</span><span class="nx">ind</span><span class="p">].</span><span class="nx">charAt</span><span class="p">(</span><span class="nx">getopt</span><span class="p">.</span><span class="nx">place</span><span class="o" style="font-weight: 600;">++</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">// character checked for validity</span></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="javascript"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nx">optopt</span> <span class="o" style="font-weight: 600;">==</span> <span class="s1" style="color: #d14;">':'</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="nx">oli</span> <span class="o" style="font-weight: 600;">=</span> <span class="nx">ostr</span><span class="p">.</span><span class="nx">indexOf</span><span class="p">(</span><span class="nx">optopt</span><span class="p">))</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="javascript"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nx">optopt</span> <span class="o" style="font-weight: 600;">==</span> <span class="s1" style="color: #d14;">'-'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">return</span> <span class="kc" style="font-weight: 600;">null</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// if the user didn't specify '-' as an option, assume it means null.</span></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="javascript"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nx">getopt</span><span class="p">.</span><span class="nx">place</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="nx">getopt</span><span class="p">.</span><span class="nx">ind</span><span class="p">;</span></span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="javascript"> <span class="k" style="font-weight: 600;">return</span> <span class="s1" style="color: #d14;">'?'</span><span class="p">;</span></span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="javascript"> <span class="p">}</span></span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="javascript"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nx">oli</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">>=</span> <span class="nx">ostr</span><span class="p">.</span><span class="nx">length</span> <span class="o" style="font-weight: 600;">||</span> <span class="nx">ostr</span><span class="p">.</span><span class="nx">charAt</span><span class="p">(</span><span class="o" style="font-weight: 600;">++</span><span class="nx">oli</span><span class="p">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s1" style="color: #d14;">':'</span><span class="p">)</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">// don't need argument</span></span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="javascript"> <span class="nx">getopt</span><span class="p">.</span><span class="nx">arg</span> <span class="o" style="font-weight: 600;">=</span> <span class="kc" style="font-weight: 600;">null</span><span class="p">;</span></span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="javascript"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nx">getopt</span><span class="p">.</span><span class="nx">place</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="nx">getopt</span><span class="p">.</span><span class="nx">place</span> <span class="o" style="font-weight: 600;">>=</span> <span class="nx">args</span><span class="p">[</span><span class="nx">getopt</span><span class="p">.</span><span class="nx">ind</span><span class="p">].</span><span class="nx">length</span><span class="p">)</span> <span class="o" style="font-weight: 600;">++</span><span class="nx">getopt</span><span class="p">.</span><span class="nx">ind</span><span class="p">,</span> <span class="nx">getopt</span><span class="p">.</span><span class="nx">place</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="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="javascript"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">// need an argument</span></span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="javascript"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nx">getopt</span><span class="p">.</span><span class="nx">place</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="nx">getopt</span><span class="p">.</span><span class="nx">place</span> <span class="o" style="font-weight: 600;"><</span> <span class="nx">args</span><span class="p">[</span><span class="nx">getopt</span><span class="p">.</span><span class="nx">ind</span><span class="p">].</span><span class="nx">length</span><span class="p">)</span></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="javascript"> <span class="nx">getopt</span><span class="p">.</span><span class="nx">arg</span> <span class="o" style="font-weight: 600;">=</span> <span class="nx">args</span><span class="p">[</span><span class="nx">getopt</span><span class="p">.</span><span class="nx">ind</span><span class="p">].</span><span class="nx">substr</span><span class="p">(</span><span class="nx">getopt</span><span class="p">.</span><span class="nx">place</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="javascript"> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nx">args</span><span class="p">.</span><span class="nx">length</span> <span class="o" style="font-weight: 600;"><=</span> <span class="o" style="font-weight: 600;">++</span><span class="nx">getopt</span><span class="p">.</span><span class="nx">ind</span><span class="p">)</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">// no arg</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="javascript"> <span class="nx">getopt</span><span class="p">.</span><span class="nx">place</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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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="javascript"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nx">ostr</span><span class="p">.</span><span class="nx">length</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="nx">ostr</span><span class="p">.</span><span class="nx">charAt</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="s1" style="color: #d14;">':'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">return</span> <span class="s1" style="color: #d14;">':'</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="31" style="width: 35px; color: rgba(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="LC31" class="line" lang="javascript"> <span class="k" style="font-weight: 600;">return</span> <span class="s1" style="color: #d14;">'?'</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="javascript"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="nx">getopt</span><span class="p">.</span><span class="nx">arg</span> <span class="o" style="font-weight: 600;">=</span> <span class="nx">args</span><span class="p">[</span><span class="nx">getopt</span><span class="p">.</span><span class="nx">ind</span><span class="p">];</span> <span class="c1" style="color: #998; font-style: italic;">// white space</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="javascript"> <span class="nx">getopt</span><span class="p">.</span><span class="nx">place</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="LC34" class="line" lang="javascript"> <span class="o" style="font-weight: 600;">++</span><span class="nx">getopt</span><span class="p">.</span><span class="nx">ind</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="javascript"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="javascript"> <span class="k" style="font-weight: 600;">return</span> <span class="nx">optopt</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="javascript"><span class="p">}</span></span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="javascript"></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="javascript"><span class="kd" style="font-weight: 600;">var</span> <span class="nx">c</span><span class="p">,</span> <span class="nx">pri_only</span> <span class="o" style="font-weight: 600;">=</span> <span class="kc" style="font-weight: 600;">false</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="javascript"><span class="k" style="font-weight: 600;">while</span> <span class="p">((</span><span class="nx">c</span> <span class="o" style="font-weight: 600;">=</span> <span class="nx">getopt</span><span class="p">(</span><span class="kr" style="font-weight: 600;">arguments</span><span class="p">,</span> <span class="s2" style="color: #d14;">"p"</span><span class="p">))</span> <span class="o" style="font-weight: 600;">!=</span> <span class="kc" style="font-weight: 600;">null</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="javascript"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nx">c</span> <span class="o" style="font-weight: 600;">==</span> <span class="s1" style="color: #d14;">'p'</span><span class="p">)</span> <span class="nx">pri_only</span> <span class="o" style="font-weight: 600;">=</span> <span class="kc" style="font-weight: 600;">true</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="javascript"></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="javascript"><span class="kd" style="font-weight: 600;">var</span> <span class="nx">file</span> <span class="o" style="font-weight: 600;">=</span> <span class="kr" style="font-weight: 600;">arguments</span><span class="p">.</span><span class="nx">length</span> <span class="o" style="font-weight: 600;">==</span> <span class="nx">getopt</span><span class="p">.</span><span class="nx">ind</span><span class="p">?</span> <span class="k" style="font-weight: 600;">new</span> <span class="nx">File</span><span class="p">()</span> <span class="p">:</span> <span class="k" style="font-weight: 600;">new</span> <span class="nx">File</span><span class="p">(</span><span class="kr" style="font-weight: 600;">arguments</span><span class="p">[</span><span class="nx">getopt</span><span class="p">.</span><span class="nx">ind</span><span class="p">]);</span></span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="javascript"><span class="kd" style="font-weight: 600;">var</span> <span class="nx">buf</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nx">Bytes</span><span class="p">();</span></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="javascript"><span class="kd" style="font-weight: 600;">var</span> <span class="nx">re</span> <span class="o" style="font-weight: 600;">=</span> <span class="sr" style="color: #009926;">/</span><span class="se" style="color: #d14;">(\d</span><span class="sr" style="color: #009926;">+</span><span class="se" style="color: #d14;">)([</span><span class="sr" style="color: #009926;">MIDSHN</span><span class="se" style="color: #d14;">])</span><span class="sr" style="color: #009926;">/g</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="javascript"><span class="kd" style="font-weight: 600;">var</span> <span class="nx">re</span> <span class="o" style="font-weight: 600;">=</span> <span class="sr" style="color: #009926;">/</span><span class="se" style="color: #d14;">(\d</span><span class="sr" style="color: #009926;">+</span><span class="se" style="color: #d14;">)([</span><span class="sr" style="color: #009926;">MIDSHN<span class="idiff left right">X=</span></span><span class="se" style="color: #d14;">])</span><span class="sr" style="color: #009926;">/g</span><span class="p">;</span></span>
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4
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="javascript"></span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="javascript"><span class="kd" style="font-weight: 600;">var</span> <span class="nx">len</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{},</span> <span class="nx">lineno</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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6
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="javascript"><span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="nx">file</span><span class="p">.</span><span class="nx">readline</span><span class="p">(</span><span class="nx">buf</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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7
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="javascript"> <span class="kd" style="font-weight: 600;">var</span> <span class="nx">m</span><span class="p">,</span> <span class="nx">line</span> <span class="o" style="font-weight: 600;">=</span> <span class="nx">buf</span><span class="p">.</span><span class="nx">toString</span><span class="p">();</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="javascript"> <span class="kd" style="font-weight: 600;">var</span> <span class="nx">m</span><span class="p">,</span> <span class="nx"><span class="idiff left">n_cigar</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">,</span></span><span class="idiff right"> </span><span class="nx">line</span> <span class="o" style="font-weight: 600;">=</span> <span class="nx">buf</span><span class="p">.</span><span class="nx">toString</span><span class="p">();</span></span>
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8
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50
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="javascript"> <span class="o" style="font-weight: 600;">++</span><span class="nx">lineno</span><span class="p">;</span></span>
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9
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<td class="diff-line-num new_line" data-linenumber="51" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
51
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="javascript"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nx">line</span><span class="p">.</span><span class="nx">charAt</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="s1" style="color: #d14;">'@'</span><span class="p">)</span> <span class="p">{</span></span>
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10
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<td class="diff-line-num new_line" data-linenumber="52" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
52
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="javascript"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="sr" style="color: #009926;">/^@SQ/</span><span class="p">.</span><span class="nx">test</span><span class="p">(</span><span class="nx">line</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="16" style="width: 35px; color: rgba(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="58" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -16,25 +58,43 @@ while (file.readline(buf) >= 0) {</td>
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16
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58
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="javascript"> <span class="p">}</span></span>
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17
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<td class="diff-line-num new_line" data-linenumber="59" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
59
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="javascript"> <span class="kd" style="font-weight: 600;">var</span> <span class="nx">t</span> <span class="o" style="font-weight: 600;">=</span> <span class="nx">line</span><span class="p">.</span><span class="nx">split</span><span class="p">(</span><span class="s2" style="color: #d14;">"</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span><span class="s2" style="color: #d14;">t"</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
18
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<td class="diff-line-num new_line" data-linenumber="60" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
60
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="javascript"> <span class="kd" style="font-weight: 600;">var</span> <span class="nx">flag</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">parseInt</span><span class="p">(</span><span class="nx">t</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="19" style="width: 35px; color: rgba(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="61" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="javascript"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nx">t</span><span class="p">[</span><span class="mi" style="color: #099;">9</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s1" style="color: #d14;">'*'</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nx">t</span><span class="p">[</span><span class="mi" style="color: #099;">10</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s1" style="color: #d14;">'*'</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nx">t</span><span class="p">[</span><span class="mi" style="color: #099;">9</span><span class="p">].</span><span class="nx">length</span> <span class="o" style="font-weight: 600;">!=</span> <span class="nx">t</span><span class="p">[</span><span class="mi" style="color: #099;">10</span><span class="p">].</span><span class="nx">length</span><span class="p">)</span> <span class="k" style="font-weight: 600;">throw</span> <span class="nb" style="color: #0086b3;">Error</span><span class="p">(</span><span class="s2" style="color: #d14;">"ERROR at line "</span> <span class="o" style="font-weight: 600;">+</span> <span class="nx">lineno</span> <span class="o" style="font-weight: 600;">+</span> <span class="s2" style="color: #d14;">": inconsistent SEQ and QUAL lengths - "</span> <span class="o" style="font-weight: 600;">+</span> <span class="nx">t</span><span class="p">[</span><span class="mi" style="color: #099;">9</span><span class="p">].</span><span class="nx">length</span> <span class="o" style="font-weight: 600;">+</span> <span class="s2" style="color: #d14;">" != "</span> <span class="o" style="font-weight: 600;">+</span> <span class="nx">t</span><span class="p">[</span><span class="mi" style="color: #099;">10</span><span class="p">].</span><span class="nx">length</span><span class="p">);</span></span>
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19
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<td class="diff-line-num new_line" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
62
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="javascript"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nx">t</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="s1" style="color: #d14;">'*'</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="nx">flag</span><span class="o" style="font-weight: 600;">&</span><span class="mi" style="color: #099;">4</span><span class="p">))</span> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="javascript"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nx">pri_only</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="nx">flag</span><span class="o" style="font-weight: 600;">&</span><span class="mh" style="color: #099;">0x100</span><span class="p">))</span> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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20
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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="javascript"> <span class="kd" style="font-weight: 600;">var</span> <span class="nx">tlen</span> <span class="o" style="font-weight: 600;">=</span> <span class="nx">len</span><span class="p">[</span><span class="nx">t</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]];</span></span>
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<td class="diff-line-num old_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
21
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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="javascript"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nx">tlen</span> <span class="o" style="font-weight: 600;">==</span> <span class="kc" style="font-weight: 600;">null</span><span class="p">)</span> <span class="k" style="font-weight: 600;">throw</span> <span class="nb" style="color: #0086b3;">Error</span><span class="p">(</span><span class="s2" style="color: #d14;">"ERROR at line "</span> <span class="o" style="font-weight: 600;">+</span> <span class="nx">lineno</span> <span class="o" style="font-weight: 600;">+</span> <span class="s2" style="color: #d14;">": can't find the length of contig "</span> <span class="o" style="font-weight: 600;">+</span> <span class="nx">t</span><span class="p">[</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="66" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="javascript"> <span class="kd" style="font-weight: 600;">var</span> <span class="nx">nn</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="nx">m</span> <span class="o" style="font-weight: 600;">=</span> <span class="sr" style="color: #009926;">/</span><span class="se" style="color: #d14;">\t</span><span class="sr" style="color: #009926;">nn:i:</span><span class="se" style="color: #d14;">(\d</span><span class="sr" style="color: #009926;">+</span><span class="se" style="color: #d14;">)</span><span class="sr" style="color: #009926;">/</span><span class="p">.</span><span class="nx">exec</span><span class="p">(</span><span class="nx">line</span><span class="p">))</span> <span class="o" style="font-weight: 600;">!=</span> <span class="kc" style="font-weight: 600;">null</span><span class="p">?</span> <span class="nb" style="color: #0086b3;">parseInt</span><span class="p">(</span><span class="nx">m</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">])</span> <span class="p">:</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
22
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<td class="diff-line-num new_line" data-linenumber="67" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
67
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="javascript"> <span class="kd" style="font-weight: 600;">var</span> <span class="nx">NM</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="nx">m</span> <span class="o" style="font-weight: 600;">=</span> <span class="sr" style="color: #009926;">/</span><span class="se" style="color: #d14;">\t</span><span class="sr" style="color: #009926;">NM:i:</span><span class="se" style="color: #d14;">(\d</span><span class="sr" style="color: #009926;">+</span><span class="se" style="color: #d14;">)</span><span class="sr" style="color: #009926;">/</span><span class="p">.</span><span class="nx">exec</span><span class="p">(</span><span class="nx">line</span><span class="p">))</span> <span class="o" style="font-weight: 600;">!=</span> <span class="kc" style="font-weight: 600;">null</span><span class="p">?</span> <span class="nb" style="color: #0086b3;">parseInt</span><span class="p">(</span><span class="nx">m</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">])</span> <span class="p">:</span> <span class="kc" style="font-weight: 600;">null</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="23" 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">
23
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<td class="diff-line-num new_line old" data-linenumber="68" 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="LC23" class="line" lang="javascript"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nx">NM</span> <span class="o" style="font-weight: 600;">==</span> <span class="kc" style="font-weight: 600;">null</span><span class="p">)</span> <span class="k" style="font-weight: 600;">throw</span> <span class="nb" style="color: #0086b3;">Error</span><span class="p">(</span><span class="s2" style="color: #d14;">"ERROR at line "</span> <span class="o" style="font-weight: 600;">+</span> <span class="nx">lineno</span> <span class="o" style="font-weight: 600;">+</span> <span class="s2" style="color: #d14;">": no NM tag"</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="24" 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">
24
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="javascript"> <span class="kd" style="font-weight: 600;">var</span> <span class="nx">clip</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="nx">I</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="nx">D</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="nx">M</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="nx">N</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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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="javascript"> <span class="kd" style="font-weight: 600;">var</span> <span class="nx">have_NM</span> <span class="o" style="font-weight: 600;">=</span> <span class="nx">NM</span> <span class="o" style="font-weight: 600;">==</span> <span class="kc" style="font-weight: 600;">null</span><span class="p">?</span> <span class="kc" style="font-weight: 600;">false</span> <span class="p">:</span> <span class="kc" style="font-weight: 600;">true</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="69" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="javascript"> <span class="nx">NM</span> <span class="o" style="font-weight: 600;">+=</span> <span class="nx">nn</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="javascript"> <span class="kd" style="font-weight: 600;">var</span> <span class="nx">clip</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="nx">I</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="nx">D</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="nx">M</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="nx">N</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="nx">ql</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="nx">tl</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="nx">mm</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="nx">ext_cigar</span> <span class="o" style="font-weight: 600;">=</span> <span class="kc" style="font-weight: 600;">false</span><span class="p">;</span></span>
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25
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71
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="javascript"> <span class="k" style="font-weight: 600;">while</span> <span class="p">((</span><span class="nx">m</span> <span class="o" style="font-weight: 600;">=</span> <span class="nx">re</span><span class="p">.</span><span class="nx">exec</span><span class="p">(</span><span class="nx">t</span><span class="p">[</span><span class="mi" style="color: #099;">5</span><span class="p">]))</span> <span class="o" style="font-weight: 600;">!=</span> <span class="kc" style="font-weight: 600;">null</span><span class="p">)</span> <span class="p">{</span></span>
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26
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72
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="javascript"> <span class="kd" style="font-weight: 600;">var</span> <span class="nx">l</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">parseInt</span><span class="p">(</span><span class="nx">m</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]);</span></span>
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27
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="javascript"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nx">m</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="s1" style="color: #d14;">'M'</span><span class="p">)</span> <span class="nx">M</span> <span class="o" style="font-weight: 600;">+=</span> <span class="nx">l</span><span class="p">;</span></span>
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28
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="javascript"> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nx">m</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="s1" style="color: #d14;">'I'</span><span class="p">)</span> <span class="o" style="font-weight: 600;">++</span><span class="nx">I</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="nx">I</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="nx">l</span><span class="p">;</span></span>
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29
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="javascript"> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nx">m</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="s1" style="color: #d14;">'D'</span><span class="p">)</span> <span class="o" style="font-weight: 600;">++</span><span class="nx">D</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="nx">D</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="nx">l</span><span class="p">;</span></span>
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30
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="javascript"> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nx">m</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="s1" style="color: #d14;">'N'</span><span class="p">)</span> <span class="nx">N</span> <span class="o" style="font-weight: 600;">+=</span> <span class="nx">l</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="31" 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">
31
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="javascript"> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nx">m</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="s1" style="color: #d14;">'S'</span> <span class="o" style="font-weight: 600;">||</span> <span class="nx">m</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="s1" style="color: #d14;">'H'</span><span class="p">)</span></span>
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32
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="javascript"> <span class="nx">clip</span><span class="p">[</span><span class="nx">M</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;">0</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="nx">l</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="33" 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">
33
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="javascript"> <span class="p">}</span></span>
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34
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="javascript"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nx">NM</span> <span class="o" style="font-weight: 600;"><</span> <span class="nx">I</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="nx">D</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">])</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="35" 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">
35
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="javascript"> <span class="nx">warn</span><span class="p">(</span><span class="s2" style="color: #d14;">"WARNING at line "</span> <span class="o" style="font-weight: 600;">+</span> <span class="nx">lineno</span> <span class="o" style="font-weight: 600;">+</span> <span class="s2" style="color: #d14;">": NM is less than the total number of gaps; skipped"</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="73" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="javascript"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nx">m</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="s1" style="color: #d14;">'M'</span><span class="p">)</span> <span class="nx">M</span> <span class="o" style="font-weight: 600;">+=</span> <span class="nx">l</span><span class="p">,</span> <span class="nx">ql</span> <span class="o" style="font-weight: 600;">+=</span> <span class="nx">l</span><span class="p">,</span> <span class="nx">tl</span> <span class="o" style="font-weight: 600;">+=</span> <span class="nx">l</span><span class="p">,</span> <span class="nx">ext_cigar</span> <span class="o" style="font-weight: 600;">=</span> <span class="kc" style="font-weight: 600;">false</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="74" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="javascript"> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nx">m</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="s1" style="color: #d14;">'I'</span><span class="p">)</span> <span class="o" style="font-weight: 600;">++</span><span class="nx">I</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="nx">I</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="nx">l</span><span class="p">,</span> <span class="nx">ql</span> <span class="o" style="font-weight: 600;">+=</span> <span class="nx">l</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="75" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="javascript"> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nx">m</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="s1" style="color: #d14;">'D'</span><span class="p">)</span> <span class="o" style="font-weight: 600;">++</span><span class="nx">D</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="nx">D</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="nx">l</span><span class="p">,</span> <span class="nx">tl</span> <span class="o" style="font-weight: 600;">+=</span> <span class="nx">l</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="76" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="javascript"> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nx">m</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="s1" style="color: #d14;">'N'</span><span class="p">)</span> <span class="nx">N</span> <span class="o" style="font-weight: 600;">+=</span> <span class="nx">l</span><span class="p">,</span> <span class="nx">tl</span> <span class="o" style="font-weight: 600;">+=</span> <span class="nx">l</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="77" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="javascript"> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nx">m</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="s1" style="color: #d14;">'S'</span><span class="p">)</span> <span class="nx">clip</span><span class="p">[</span><span class="nx">M</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;">0</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="nx">l</span><span class="p">,</span> <span class="nx">ql</span> <span class="o" style="font-weight: 600;">+=</span> <span class="nx">l</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="78" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="javascript"> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nx">m</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="s1" style="color: #d14;">'H'</span><span class="p">)</span> <span class="nx">clip</span><span class="p">[</span><span class="nx">M</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;">0</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="nx">l</span><span class="p">;</span></span>
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<td class="diff-line-num new old_line" data-linenumber="36" style="width: 35px; color: rgba(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="79" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="javascript"> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nx">m</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="s1" style="color: #d14;">'='</span><span class="p">)</span> <span class="nx">M</span> <span class="o" style="font-weight: 600;">+=</span> <span class="nx">l</span><span class="p">,</span> <span class="nx">ql</span> <span class="o" style="font-weight: 600;">+=</span> <span class="nx">l</span><span class="p">,</span> <span class="nx">tl</span> <span class="o" style="font-weight: 600;">+=</span> <span class="nx">l</span><span class="p">,</span> <span class="nx">ext_cigar</span> <span class="o" style="font-weight: 600;">=</span> <span class="kc" style="font-weight: 600;">true</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="80" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="javascript"> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nx">m</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="s1" style="color: #d14;">'X'</span><span class="p">)</span> <span class="nx">M</span> <span class="o" style="font-weight: 600;">+=</span> <span class="nx">l</span><span class="p">,</span> <span class="nx">ql</span> <span class="o" style="font-weight: 600;">+=</span> <span class="nx">l</span><span class="p">,</span> <span class="nx">tl</span> <span class="o" style="font-weight: 600;">+=</span> <span class="nx">l</span><span class="p">,</span> <span class="nx">mm</span> <span class="o" style="font-weight: 600;">+=</span> <span class="nx">l</span><span class="p">,</span> <span class="nx">ext_cigar</span> <span class="o" style="font-weight: 600;">=</span> <span class="kc" style="font-weight: 600;">true</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="javascript"> <span class="o" style="font-weight: 600;">++</span><span class="nx">n_cigar</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="82" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="javascript"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="83" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="javascript"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nx">n_cigar</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">65535</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="84" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="javascript"> <span class="nx">warn</span><span class="p">(</span><span class="s2" style="color: #d14;">"WARNING at line "</span> <span class="o" style="font-weight: 600;">+</span> <span class="nx">lineno</span> <span class="o" style="font-weight: 600;">+</span> <span class="s2" style="color: #d14;">": "</span> <span class="o" style="font-weight: 600;">+</span> <span class="nx">n_cigar</span> <span class="o" style="font-weight: 600;">+</span> <span class="s2" style="color: #d14;">" CIGAR operations"</span><span class="p">);</span></span>
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<td class="diff-line-num new old_line" data-linenumber="36" style="width: 35px; color: rgba(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="85" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="javascript"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nx">tl</span> <span class="o" style="font-weight: 600;">+</span> <span class="nb" style="color: #0086b3;">parseInt</span><span class="p">(</span><span class="nx">t</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">])</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">></span> <span class="nx">tlen</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="86" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="javascript"> <span class="nx">warn</span><span class="p">(</span><span class="s2" style="color: #d14;">"WARNING at line "</span> <span class="o" style="font-weight: 600;">+</span> <span class="nx">lineno</span> <span class="o" style="font-weight: 600;">+</span> <span class="s2" style="color: #d14;">": alignment end position larger than ref length; skipped"</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
36
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<td class="diff-line-num new_line" data-linenumber="87" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
87
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<pre style="margin: 0;"> <span id="LC87" class="line" lang="javascript"> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
37
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<td class="diff-line-num new_line" data-linenumber="88" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
88
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="javascript"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="89" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="javascript"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nx">t</span><span class="p">[</span><span class="mi" style="color: #099;">9</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s1" style="color: #d14;">'*'</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nx">t</span><span class="p">[</span><span class="mi" style="color: #099;">9</span><span class="p">].</span><span class="nx">length</span> <span class="o" style="font-weight: 600;">!=</span> <span class="nx">ql</span><span class="p">)</span> <span class="p">{</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="90" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="javascript"> <span class="nx">warn</span><span class="p">(</span><span class="s2" style="color: #d14;">"WARNING at line "</span> <span class="o" style="font-weight: 600;">+</span> <span class="nx">lineno</span> <span class="o" style="font-weight: 600;">+</span> <span class="s2" style="color: #d14;">": SEQ length inconsistent with CIGAR ("</span> <span class="o" style="font-weight: 600;">+</span> <span class="nx">t</span><span class="p">[</span><span class="mi" style="color: #099;">9</span><span class="p">].</span><span class="nx">length</span> <span class="o" style="font-weight: 600;">+</span> <span class="s2" style="color: #d14;">" != "</span> <span class="o" style="font-weight: 600;">+</span> <span class="nx">ql</span> <span class="o" style="font-weight: 600;">+</span> <span class="s2" style="color: #d14;">"); skipped"</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="91" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="javascript"> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="javascript"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="93" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="javascript"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="nx">have_NM</span> <span class="o" style="font-weight: 600;">||</span> <span class="nx">ext_cigar</span><span class="p">)</span> <span class="nx">NM</span> <span class="o" style="font-weight: 600;">=</span> <span class="nx">I</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="nx">D</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="nx">mm</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="94" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="javascript"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nx">NM</span> <span class="o" style="font-weight: 600;"><</span> <span class="nx">I</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="nx">D</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="nx">mm</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="95" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="javascript"> <span class="nx">warn</span><span class="p">(</span><span class="s2" style="color: #d14;">"WARNING at line "</span> <span class="o" style="font-weight: 600;">+</span> <span class="nx">lineno</span> <span class="o" style="font-weight: 600;">+</span> <span class="s2" style="color: #d14;">": NM is less than the total number of gaps ("</span> <span class="o" style="font-weight: 600;">+</span> <span class="nx">NM</span> <span class="o" style="font-weight: 600;">+</span> <span class="s2" style="color: #d14;">" < "</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="nx">I</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="nx">D</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="nx">mm</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s2" style="color: #d14;">")"</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="javascript"> <span class="nx">NM</span> <span class="o" style="font-weight: 600;">=</span> <span class="nx">I</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="nx">D</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="nx">mm</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="javascript"> <span class="p">}</span></span>
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38
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<td class="diff-line-num new_line" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
98
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<pre style="margin: 0;"> <span id="LC98" class="line" lang="javascript"> <span class="kd" style="font-weight: 600;">var</span> <span class="nx">extra</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s2" style="color: #d14;">"mm:i:"</span><span class="o" style="font-weight: 600;">+</span><span class="p">(</span><span class="nx">NM</span><span class="o" style="font-weight: 600;">-</span><span class="nx">I</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="nx">D</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]),</span> <span class="s2" style="color: #d14;">"io:i:"</span><span class="o" style="font-weight: 600;">+</span><span class="nx">I</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="s2" style="color: #d14;">"in:i:"</span><span class="o" style="font-weight: 600;">+</span><span class="nx">I</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">],</span> <span class="s2" style="color: #d14;">"do:i:"</span><span class="o" style="font-weight: 600;">+</span><span class="nx">D</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="s2" style="color: #d14;">"dn:i:"</span><span class="o" style="font-weight: 600;">+</span><span class="nx">D</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 old_line" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
39
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<td class="diff-line-num new_line" data-linenumber="99" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
99
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="javascript"> <span class="kd" style="font-weight: 600;">var</span> <span class="nx">match</span> <span class="o" style="font-weight: 600;">=</span> <span class="nx">M</span> <span class="o" style="font-weight: 600;">-</span> <span class="p">(</span><span class="nx">NM</span> <span class="o" style="font-weight: 600;">-</span> <span class="nx">I</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="nx">D</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 old_line" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
40
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<td class="diff-line-num new_line" data-linenumber="100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
100
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="javascript"> <span class="kd" style="font-weight: 600;">var</span> <span class="nx">blen</span> <span class="o" style="font-weight: 600;">=</span> <span class="nx">M</span> <span class="o" style="font-weight: 600;">+</span> <span class="nx">I</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="nx">D</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">];</span></span>
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<a href="https://salsa.debian.org/med-team/miniasm/compare/c23b2121ec3f8082bbb02499edea827181a76fda...d7b6c4f3557ddd7602088589e02ff4ef9e874444#e311dec91606c22084cc17eb781191d38d7cd6c2"><strong>misc/wt2paf.pl</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">#!/usr/bin/env perl</span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="perl"></span>
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<td class="diff-line-num new new_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">
3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nv" style="color: teal;">strict</span><span class="p">;</span></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nv" style="color: teal;">warnings</span><span class="p">;</span></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="perl"></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="perl"><span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="o" style="font-weight: 600;"><></span><span class="p">)</span> <span class="p">{</span></span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">chomp</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">@t</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">split</span><span class="p">(</span><span class="s" style="color: #d14;">"\t"</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="9" style="width: 35px; color: rgba(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="LC9" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: teal;">$t</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="s" style="color: #d14;">'-'</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="perl"> <span class="nv" style="color: teal;">@t</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">,</span><span class="mi" style="color: #099;">4</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="nv" style="color: teal;">$t</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="nv" style="color: teal;">$t</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">],</span> <span class="nv" style="color: teal;">$t</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="nv" style="color: teal;">$t</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="perl"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: teal;">$t</span><span class="p">[</span><span class="mi" style="color: #099;">6</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="s" style="color: #d14;">'-'</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="13" style="width: 35px; color: rgba(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="LC13" class="line" lang="perl"> <span class="nv" style="color: teal;">@t</span><span class="p">[</span><span class="mi" style="color: #099;">8</span><span class="p">,</span><span class="mi" style="color: #099;">9</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="nv" style="color: teal;">$t</span><span class="p">[</span><span class="mi" style="color: #099;">7</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="nv" style="color: teal;">$t</span><span class="p">[</span><span class="mi" style="color: #099;">9</span><span class="p">],</span> <span class="nv" style="color: teal;">$t</span><span class="p">[</span><span class="mi" style="color: #099;">7</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="nv" style="color: teal;">$t</span><span class="p">[</span><span class="mi" style="color: #099;">8</span><span class="p">]);</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="perl"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$bl</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$t</span><span class="p">[</span><span class="mi" style="color: #099;">12</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="nv" style="color: teal;">$t</span><span class="p">[</span><span class="mi" style="color: #099;">13</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="nv" style="color: teal;">$t</span><span class="p">[</span><span class="mi" style="color: #099;">14</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="nv" style="color: teal;">$t</span><span class="p">[</span><span class="mi" style="color: #099;">15</span><span class="p">];</span></span>
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<td class="diff-line-num new new_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="nb" style="color: #0086b3;">join</span><span class="p">(</span><span class="s" style="color: #d14;">"\t"</span><span class="p">,</span> <span class="nv" style="color: teal;">@t</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">2</span><span class="o" style="font-weight: 600;">..</span><span class="mi" style="color: #099;">4</span><span class="p">],</span> <span class="nv" style="color: teal;">$t</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="nv" style="color: teal;">$t</span><span class="p">[</span><span class="mi" style="color: #099;">6</span><span class="p">]?</span> <span class="s" style="color: #d14;">'+'</span> <span class="p">:</span> <span class="s" style="color: #d14;">'-'</span><span class="p">,</span> <span class="nv" style="color: teal;">@t</span><span class="p">[</span><span class="mi" style="color: #099;">5</span><span class="p">,</span><span class="mi" style="color: #099;">7</span><span class="o" style="font-weight: 600;">..</span><span class="mi" style="color: #099;">9</span><span class="p">,</span><span class="mi" style="color: #099;">12</span><span class="p">],</span> <span class="nv" style="color: teal;">$bl</span><span class="p">,</span> <span class="mi" style="color: #099;">255</span><span class="p">),</span> <span class="s" style="color: #d14;">"\n"</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="perl"><span class="p">}</span></span></pre>
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