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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/fermi-lite">Debian Med / fermi-lite</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/fermi-lite/-/commit/85d2a97c3ff9fd8f87df47b979831db3b23bf726">85d2a97c</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2021-01-08T10:42:40+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Switch to upstream HEAD using gitmode in watch file
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/fermi-lite/-/commit/64754d1a69ca6caa081d83627a6988ecd7fb09d8">64754d1a</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2021-01-08T10:42:56+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 0.1+git20190320.b499514</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/fermi-lite/-/commit/04b0685c79e2cdef6dfd3473c4a16ff8b51fac55">04b0685c</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2021-01-08T10:42:56+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/0.1+git20190320.b499514'
Update to upstream version '0.1+git20190320.b499514'
with Debian dir cbae21d2da60fec342db6bc73e89d9da0e7a112b</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/fermi-lite/-/commit/57245fb8a59717d5c5fdbc7b865d00ad75c5852a">57245fb8</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2021-01-08T10:46:39+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update patches
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/fermi-lite/-/commit/1c85ecbd6bab750c832899a40b522aa8e0bd6814">1c85ecbd</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2021-01-08T10:47:28+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Standards-Version: 4.5.1
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/fermi-lite/-/commit/5366ecf1ac7aea17b889e291c9763f0cc4fb2887">5366ecf1</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2021-01-08T10:47:28+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: debhelper-compat 13
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/fermi-lite/-/commit/24bfe49e5975666ec6bf6691c37b7ee0cc844aa1">24bfe49e</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2021-01-08T10:49:15+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Ready to upload to unstable
</pre>
</li>
</ul>
<h4>11 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
README.md
</a>
</li>
<li class="file-stats">
<a href="#724704cd786e5dfc8b364ff072252e8515b801c3">
bubble.c
</a>
</li>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
</a>
</li>
<li class="file-stats">
<a href="#11eaa378da7ca1bd550753bd61b39f12e0453cac">
debian/patches/rename_bseq1_t.patch
</a>
</li>
<li class="file-stats">
<a href="#68ef9f98c01c7eecd4c605cc26048a06f3304b79">
debian/watch
</a>
</li>
<li class="file-stats">
<a href="#d5b1ef39d032b550cec6ec1007b182e41ada7193">
example.c
</a>
</li>
<li class="file-stats">
<a href="#53398c4acc0cae64b87e357193c54e2042eaa019">
fml.h
</a>
</li>
<li class="file-stats">
<a href="#6bae174381d2d3da5bf4d20b215570420226d9cc">
mag.c
</a>
</li>
<li class="file-stats">
<a href="#276dcdf4b383e79a86bb74ce20195cee3a958ae8">
mag.h
</a>
</li>
<li class="file-stats">
<a href="#c6126a1e83607d3fdd02ded564d99e9f160cf712">
misc.c
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
<a href="https://salsa.debian.org/med-team/fermi-lite/-/compare/a3135da8ba6e517fb54a0f3950c62653e80783e7...24bfe49e5975666ec6bf6691c37b7ee0cc844aa1#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d"><strong>README.md</strong></a>
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<td class="diff-line-num unfold js-unfold new_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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -18,6 +18,11 @@ is able to retain heterozygous events and thus can be used to assemble diploid</td>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="markdown">regions for the purpose of variant calling. It is one of the limited choices</span>
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<td class="diff-line-num old_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="markdown">for local re-assembly and arguably the easiest to interface.</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC20" class="line" lang="markdown"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="21" style="width: 35px; color: rgba(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="LC21" class="line" lang="markdown">If you use fermi-lite in your work, please cite the FermiKit paper:</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="markdown"></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="21" style="width: 35px; color: rgba(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="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="markdown"><span class="gt" style="color: #a00;">> Li H (2015) FermiKit: assembly-based variant calling for Illumina</span></span>
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<td class="diff-line-num new new_line" data-linenumber="24" style="width: 35px; color: rgba(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="LC24" class="line" lang="markdown"><span class="gt" style="color: #a00;">> resequencing data, *Bioinformatics*, **31**:3694-6.</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">
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="markdown"></span>
</pre>
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<td class="diff-line-num new_line" data-linenumber="26" style="width: 35px; color: rgba(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="LC26" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Usage</span></span>
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<td class="diff-line-num new_line" data-linenumber="27" style="width: 35px; color: rgba(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="LC27" class="line" lang="markdown"></span>
</pre>
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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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<td class="diff-line-num new_line" data-linenumber="28" style="width: 35px; color: rgba(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="LC28" class="line" lang="markdown">For now, see <span class="p">[</span><span class="nv" style="color: #008080;">example.c</span><span class="p">][</span><span class="ss" style="color: #990073;">example</span><span class="p">]</span> for the basic use of the library. Here is a</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="42" style="width: 35px; color: rgba(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="47" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -42,8 +47,9 @@ int main(int argc, char *argv[])</td>
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<td class="diff-line-num new_line" data-linenumber="47" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="markdown"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="markdown"><span class="p">}</span></span>
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<td class="diff-line-num new_line" data-linenumber="49" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="markdown"><span class="p">```</span></span>
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<td class="diff-line-num old old_line" data-linenumber="45" 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="LC45" class="line" lang="markdown">The direct assembly output is in fact a graph. You may have a look at the</span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">header file</span><span class="p">][</span><span class="ss" style="color: #990073;">header</span><span class="p">]</span> for details.</span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="markdown">The <span class="sb" style="color: #d14;">`fml_assemble()`</span> output is in fact a graph. You may have a look at the</span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="markdown"><span class="sb" style="color: #d14;">`fml_utg_print_gfa()`</span> function in <span class="p">[</span><span class="nv" style="color: #008080;">misc.c</span><span class="p">][</span><span class="ss" style="color: #990073;">misc</span><span class="p">]</span> about how to derive a</span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">GFA</span><span class="p">][</span><span class="ss" style="color: #990073;">gfa</span><span class="p">]</span> representation from an array of <span class="sb" style="color: #d14;">`fml_utg_t`</span> objects.</span>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Overview of the Assembly Algorithm</span></span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="markdown"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="86" style="width: 35px; color: rgba(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="92" style="width: 35px; color: rgba(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">@@ -86,3 +92,5 @@ after these procedure is the final output. Sequences in this graph are unitigs.</td>
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="markdown"><span class="p">[</span><span class="ss" style="color: #990073;">fk</span><span class="p">]:</span> <span class="sx" style="color: #d14;">http://github.com/lh3/fermikit</span></span>
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<pre style="margin: 0;"> <span id="LC93" class="line" lang="markdown"><span class="p">[</span><span class="ss" style="color: #990073;">example</span><span class="p">]:</span> <span class="sx" style="color: #d14;">https://github.com/lh3/fermi-lite/blob/master/example.c</span></span>
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<pre style="margin: 0;"> <span id="LC94" class="line" lang="markdown"><span class="p">[</span><span class="ss" style="color: #990073;">header</span><span class="p">]:</span> <span class="sx" style="color: #d14;">https://github.com/lh3/fermi-lite/blob/master/fml.h</span></span>
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="markdown"><span class="p">[</span><span class="ss" style="color: #990073;">misc</span><span class="p">]:</span> <span class="sx" style="color: #d14;">https://github.com/lh3/fermi-lite/blob/master/misc.c</span></span>
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="markdown"><span class="p">[</span><span class="ss" style="color: #990073;">gfa</span><span class="p">]:</span> <span class="sx" style="color: #d14;">https://github.com/pmelsted/GFA-spec</span></span></pre>
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<li id="724704cd786e5dfc8b364ff072252e8515b801c3">
<a href="https://salsa.debian.org/med-team/fermi-lite/-/compare/a3135da8ba6e517fb54a0f3950c62653e80783e7...24bfe49e5975666ec6bf6691c37b7ee0cc844aa1#724704cd786e5dfc8b364ff072252e8515b801c3"><strong>bubble.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">@@ -16,8 +16,6 @@ typedef khash_t(64) hash64_t;</td>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define edge_mark_del(_x) ((_x).x = (uint64_t)-2, (_x).y = 0)</span></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define edge_is_del(_x) ((_x).x == (uint64_t)-2 || (_x).y == 0)</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="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">fm_verbose</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/******************</span></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * Closed bubbles *</span></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> ******************/</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="178" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="176" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -178,7 +176,7 @@ void mag_g_simplify_bubble(mag_t *g, int max_vtx, int max_dist)</td>
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<pre style="margin: 0;"> <span id="LC176" class="line" lang="c"> <span class="n" style="color: #333;">mag_g_merge</span><span class="p">(</span><span class="n" style="color: #333;">g</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>
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<pre style="margin: 0;"> <span id="LC177" class="line" lang="c"><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>
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<pre style="margin: 0;">-<span id="LC181" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">mag_vh_pop_simple</span><span class="p">(</span><span class="n" style="color: #333;">mag_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">g</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">idd</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">max_cov</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">max_frac</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">aggressive</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="179" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">mag_vh_pop_simple</span><span class="p">(</span><span class="n" style="color: #333;">mag_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">g</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint64_t</span> <span class="n" style="color: #333;">idd</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">max_cov</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">max_frac</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;"><span class="idiff left">max_bdiff</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">int</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">aggressive</span><span class="p">)</span></span>
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182
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180
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<pre style="margin: 0;"> <span id="LC180" class="line" lang="c"><span class="p">{</span></span>
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183
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181
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<pre style="margin: 0;"> <span id="LC181" class="line" lang="c"> <span class="n" style="color: #333;">magv_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;">v</span><span class="p">.</span><span class="n" style="color: #333;">a</span><span class="p">[</span><span class="n" style="color: #333;">idd</span><span class="o" style="font-weight: 600;">>></span><span class="mi" style="color: #099;">1</span><span class="p">],</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">q</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">];</span></span>
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184
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182
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<pre style="margin: 0;"> <span id="LC182" class="line" lang="c"> <span class="n" style="color: #333;">ku128_v</span> <span class="o" style="font-weight: 600;">*</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="195" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -195,9 +193,10 @@ int mag_vh_pop_simple(mag_t *g, uint64_t idd, float max_cov, float max_frac, int</td>
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195
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193
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<pre style="margin: 0;"> <span id="LC193" class="line" lang="c"> <span class="n" style="color: #333;">dir</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">&</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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196
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194
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<pre style="margin: 0;"> <span id="LC194" class="line" lang="c"> <span class="n" style="color: #333;">q</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="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;">v</span><span class="p">.</span><span class="n" style="color: #333;">a</span><span class="p">[</span><span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">>></span><span class="mi" style="color: #099;">1</span><span class="p">];</span></span>
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197
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195
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<pre style="margin: 0;"> <span id="LC195" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">q</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">nei</span><span class="p">[</span><span class="mi" style="color: #099;">0</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="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">q</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">nei</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">].</span><span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">ret</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// no bubble</span></span>
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198
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<pre style="margin: 0;">-<span id="LC198" class="line" lang="c"> <span class="n" style="color: #333;">l</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">q</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">len</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;">q</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">nei</span><span class="p">[</span><span class="mi" style="color: #099;">0</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;">y</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">q</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">nei</span><span class="p">[</span><span class="mi" style="color: #099;">1</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;">y</span><span class="p">);</span></span>
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196
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="c"> <span class="n" style="color: #333;">l</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">q</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">len</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;">q</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">nei</span><span class="p">[</span><span class="mi" style="color: #099;">0</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;">y</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">q</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">nei</span><span class="p">[</span><span class="mi" style="color: #099;">1</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;">y</span><span class="p">);</span><span class="idiff left"> </span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right">// bubble length, excluding overlaps</span></span></span>
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199
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197
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<pre style="margin: 0;"> <span id="LC197" class="line" lang="c"> <span class="p">}</span></span>
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200
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198
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<pre style="margin: 0;"> <span id="LC198" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">q</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;">nei</span><span class="p">[</span><span class="n" style="color: #333;">dir</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 class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">q</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;">nei</span><span class="p">[</span><span class="n" style="color: #333;">dir</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 class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">x</span><span class="p">)</span> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">ret</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// no bubble</span></span>
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">l</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;">l</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;">max_bdiff</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">l</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;">l</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;">max_bdiff</span><span class="p">)</span> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// huge bubble differences</span></span>
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201
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<pre style="margin: 0;"> <span id="LC200" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">2</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 class="c1" style="color: #998; font-style: italic;">// set seq[] and cov[], and compute avg[]</span></span>
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<pre style="margin: 0;"> <span id="LC201" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">l</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC202" class="line" lang="c"> <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="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">malloc</span><span class="p">(</span><span class="n" style="color: #333;">l</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span><span class="o" style="font-weight: 600;"><<</span><span class="mi" style="color: #099;">1</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">@@ -254,16 +253,16 @@ int mag_vh_pop_simple(mag_t *g, uint64_t idd, float max_cov, float max_frac, int</td>
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<pre style="margin: 0;"> <span id="LC253" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">ret</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC254" class="line" lang="c"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC255" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC257" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">mag_g_pop_simple</span><span class="p">(</span><span class="n" style="color: #333;">mag_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">g</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">max_cov</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">max_frac</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">min_merge_len</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">aggressive</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC256" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">mag_g_pop_simple</span><span class="p">(</span><span class="n" style="color: #333;">mag_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">g</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">max_cov</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">max_frac</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">min_merge_len</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;"><span class="idiff left">max_bdiff</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">int</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">aggressive</span><span class="p">)</span></span>
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258
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<pre style="margin: 0;"> <span id="LC257" class="line" lang="c"><span class="p">{</span></span>
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259
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<pre style="margin: 0;"> <span id="LC258" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int64_t</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">n_examined</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;">n_popped</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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260
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<pre style="margin: 0;"> <span id="LC259" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ret</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC260" class="line" lang="c"></span>
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262
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<pre style="margin: 0;"> <span id="LC261" 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;">g</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">v</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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<td class="diff-line-num old old_line" data-linenumber="263" 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">
263
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<pre style="margin: 0;">-<span id="LC263" class="line" lang="c"> <span class="n" style="color: #333;">ret</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mag_vh_pop_simple</span><span class="p">(</span><span class="n" style="color: #333;">g</span><span class="p">,</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;"><<</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">|</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">max_cov</span><span class="p">,</span> <span class="n" style="color: #333;">max_frac</span><span class="p">,</span> <span class="n" style="color: #333;">aggressive</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC262" class="line" lang="c"> <span class="n" style="color: #333;">ret</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mag_vh_pop_simple</span><span class="p">(</span><span class="n" style="color: #333;">g</span><span class="p">,</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;"><<</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">|</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">max_cov</span><span class="p">,</span> <span class="n" style="color: #333;">max_frac</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">max_bdiff</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">aggressive</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC263" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">ret</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">n_examined</span><span class="p">;</span></span>
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265
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<td class="diff-line-num new_line" data-linenumber="264" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
264
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<pre style="margin: 0;"> <span id="LC264" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">ret</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;">n_popped</span><span class="p">;</span></span>
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266
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<pre style="margin: 0;">-<span id="LC266" class="line" lang="c"> <span class="n" style="color: #333;">ret</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mag_vh_pop_simple</span><span class="p">(</span><span class="n" style="color: #333;">g</span><span class="p">,</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;"><<</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">|</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">max_cov</span><span class="p">,</span> <span class="n" style="color: #333;">max_frac</span><span class="p">,</span> <span class="n" style="color: #333;">aggressive</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC265" class="line" lang="c"> <span class="n" style="color: #333;">ret</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mag_vh_pop_simple</span><span class="p">(</span><span class="n" style="color: #333;">g</span><span class="p">,</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;"><<</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">|</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">max_cov</span><span class="p">,</span> <span class="n" style="color: #333;">max_frac</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">max_bdiff</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">aggressive</span><span class="p">);</span></span>
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267
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266
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<pre style="margin: 0;"> <span id="LC266" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">ret</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">n_examined</span><span class="p">;</span></span>
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267
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<pre style="margin: 0;"> <span id="LC267" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">ret</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;">n_popped</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC268" class="line" lang="c"> <span class="p">}</span></span>
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<a href="https://salsa.debian.org/med-team/fermi-lite/-/compare/a3135da8ba6e517fb54a0f3950c62653e80783e7...24bfe49e5975666ec6bf6691c37b7ee0cc844aa1#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">fermi-lite (0.1<span class="idiff left right">-14) UNRELEASED</span>; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">fermi-lite (0.1<span class="idiff left right">+git20190320.b499514-1) 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"> [ Michael R. Crusoe ]</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"> * Team upload.</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> * Switch to upstream HEAD using gitmode in watch file</span>
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext"> * Remove trailing whitespace in debian/changelog (routine-update)</span>
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7
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"> * Use the libsimde-dev package instead of our code copy</span>
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6
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8
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext"> -- Michael R. Crusoe <michael.crusoe@gmail.com> Mon, 20 Apr 2020 12:54:26 +0200</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> [ Andreas Tille ]</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> * Standards-Version: 4.5.1 (routine-update)</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> * debhelper-compat 13 (routine-update)</span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Fri, 08 Jan 2021 10:47:39 +0100</span>
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14
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">fermi-lite (0.1-13) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"></span>
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<a href="https://salsa.debian.org/med-team/fermi-lite/-/compare/a3135da8ba6e517fb54a0f3950c62653e80783e7...24bfe49e5975666ec6bf6691c37b7ee0cc844aa1#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</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">@@ -3,12 +3,12 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.</td>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">Uploaders: Sascha Steinbiss <satta@debian.org>, Nilesh Patra <npatra974@gmail.com></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">Section: science</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Priority: optional</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext">Build-Depends: debhelper-compat (= 1<span class="idiff left right">2</span>),</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">Build-Depends: debhelper-compat (= 1<span class="idiff left right">3</span>),</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"> d-shlibs,</span>
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8
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> zlib1g-dev,</span>
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9
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> libsimde-dev,</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> help2man</span>
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11
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext">Standards-Version: 4.5.<span class="idiff left right">0</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">Standards-Version: 4.5.<span class="idiff left right">1</span></span>
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12
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/fermi-lite</span>
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13
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/fermi-lite.git</span>
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14
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">Homepage: https://github.com/lh3/fermi-lite</span>
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<li id="11eaa378da7ca1bd550753bd61b39f12e0453cac">
<a href="https://salsa.debian.org/med-team/fermi-lite/-/compare/a3135da8ba6e517fb54a0f3950c62653e80783e7...24bfe49e5975666ec6bf6691c37b7ee0cc844aa1#11eaa378da7ca1bd550753bd61b39f12e0453cac"><strong>debian/patches/rename_bseq1_t.patch</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">@@ -109,7 +109,7 @@ Last-Update: Thu, 02 Feb 2017 10:57:56 +0100</td>
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<pre style="margin: 0;"> <span id="LC109" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/misc.c</span></span>
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<pre style="margin: 0;"> <span id="LC110" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/misc.c</span></span>
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<pre style="margin: 0;"> <span id="LC111" class="line" lang="diff"><span class="p">@@ -40,7 +40,7 @@</span> void fml_opt_init(fml_opt_t *opt)</span>
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<pre style="margin: 0;">-<span id="LC112" class="line" lang="diff"> opt->mag_opt.flag = MAG_F_NO_SIMPL;</span>
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="diff"> opt->mag_opt.flag = MAG_F_NO_SIMPL<span class="idiff left right"> | MAG_F_POPOPEN</span>;</span>
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<pre style="margin: 0;"> <span id="LC113" class="line" lang="diff"> }</span>
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<pre style="margin: 0;"> <span id="LC114" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC115" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-void fml_opt_adjust(fml_opt_t *opt, int n_seqs, const bseq1_t *seqs)</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">@@ -126,7 +126,7 @@ Last-Update: Thu, 02 Feb 2017 10:57:56 +0100</td>
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126
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<pre style="margin: 0;"> <span id="LC126" class="line" lang="diff"> {</span>
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127
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127
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<pre style="margin: 0;"> <span id="LC127" class="line" lang="diff"> mrope_t *mr;</span>
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128
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<pre style="margin: 0;"> <span id="LC128" class="line" lang="diff"> kstring_t str = {0,0,0};</span>
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129
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<pre style="margin: 0;">-<span id="LC129" class="line" lang="diff"><span class="p">@@ -<span class="idiff left right">75,7 +75</span>,7 @@</span> struct rld_t *fml_fmi_gen(int n, bseq1_t</span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="diff"><span class="p">@@ -<span class="idiff left right">80,7 +80</span>,7 @@</span> struct rld_t *fml_fmi_gen(int n, bseq1_t</span>
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130
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<pre style="margin: 0;"> <span id="LC130" class="line" lang="diff"> mr = mr_init(ROPE_DEF_MAX_NODES, ROPE_DEF_BLOCK_LEN, MR_SO_RCLO);</span>
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131
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<pre style="margin: 0;"> <span id="LC131" class="line" lang="diff"> for (k = 0; k < n; ++k) {</span>
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<pre style="margin: 0;"> <span id="LC132" class="line" lang="diff"> int 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">@@ -135,7 +135,7 @@ Last-Update: Thu, 02 Feb 2017 10:57:56 +0100</td>
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<pre style="margin: 0;"> <span id="LC135" class="line" lang="diff"> if (s->l_seq == 0) continue;</span>
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136
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<pre style="margin: 0;"> <span id="LC136" class="line" lang="diff"> free(s->qual);</span>
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<pre style="margin: 0;"> <span id="LC137" class="line" lang="diff"> for (i = 0; i < s->l_seq; ++i)</span>
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138
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<pre style="margin: 0;">-<span id="LC138" class="line" lang="diff"><span class="p">@@ -1<span class="idiff left right">16,7 +116</span>,7 @@</span> struct rld_t *fml_fmi_gen(int n, bseq1_t</span>
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="diff"><span class="p">@@ -1<span class="idiff left right">21,7 +121</span>,7 @@</span> struct rld_t *fml_fmi_gen(int n, bseq1_t</span>
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139
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139
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<pre style="margin: 0;"> <span id="LC139" class="line" lang="diff"> return e;</span>
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140
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<pre style="margin: 0;"> <span id="LC140" class="line" lang="diff"> }</span>
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<pre style="margin: 0;"> <span id="LC141" class="line" lang="diff"> </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">@@ -144,7 +144,7 @@ Last-Update: Thu, 02 Feb 2017 10:57:56 +0100</td>
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144
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<pre style="margin: 0;"> <span id="LC144" class="line" lang="diff"> {</span>
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<pre style="margin: 0;"> <span id="LC145" class="line" lang="diff"> return fml_fmi_gen(n, seq, opt->n_threads > 1? 1 : 0);</span>
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146
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146
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<pre style="margin: 0;"> <span id="LC146" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">-<span id="LC147" class="line" lang="diff"><span class="p">@@ -2<span class="idiff left right">51,7 +251</span>,7 @@</span> void fml_utg_destroy(int n, fml_utg_t *u</span>
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="diff"><span class="p">@@ -2<span class="idiff left right">77,7 +277</span>,7 @@</span> void fml_utg_destroy(int n, fml_utg_t *u</span>
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<pre style="margin: 0;"> <span id="LC148" class="line" lang="diff"> </span>
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149
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149
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<pre style="margin: 0;"> <span id="LC149" class="line" lang="diff"> #define MAG_MIN_NSR_COEF .1</span>
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<pre style="margin: 0;"> <span id="LC150" class="line" lang="diff"> </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">@@ -158,21 +158,21 @@ Last-Update: Thu, 02 Feb 2017 10:57:56 +0100</td>
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158
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<pre style="margin: 0;"> <span id="LC158" class="line" lang="diff"><span class="p">@@ -7,7 +7,7 @@</span> int main(int argc, char *argv[])</span>
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159
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<pre style="margin: 0;"> <span id="LC159" class="line" lang="diff"> {</span>
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<pre style="margin: 0;"> <span id="LC160" class="line" lang="diff"> fml_opt_t opt;</span>
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161
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<pre style="margin: 0;">-<span id="LC161" class="line" lang="diff"> int c, n_seqs, n_utg;</span>
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="diff"> int c, n_seqs, n_utg<span class="idiff left right">, gfa_out = 0</span>;</span>
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<pre style="margin: 0;"> <span id="LC162" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- bseq1_t *seqs;</span></span>
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<pre style="margin: 0;"> <span id="LC163" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ fml_seq1_t *seqs;</span></span>
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<pre style="margin: 0;"> <span id="LC164" class="line" lang="diff"> fml_utg_t *utg;</span>
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<pre style="margin: 0;"> <span id="LC165" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC166" class="line" lang="diff"> fml_opt_init(&opt);</span>
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167
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<pre style="margin: 0;">-<span id="LC167" class="line" lang="diff"><span class="p">@@ -<span class="idiff left right">34,7 +34</span>,7 @@</span> int main(int argc, char *argv[])</span>
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168
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<pre style="margin: 0;">-<span id="LC168" class="line" lang="diff"> fprintf(stderr, " -<span class="idiff left right">A discard heterozygotes (apply this to assemble bacterial genomes)</span>\n");</span>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="diff"><span class="p">@@ -<span class="idiff left right">41,7 +41</span>,7 @@</span> int main(int argc, char *argv[])</span>
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="diff"> fprintf(stderr, " -<span class="idiff left right">g output the assembly graph in the GFA format</span>\n");</span>
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169
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169
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<pre style="margin: 0;"> <span id="LC169" class="line" lang="diff"> return 1;</span>
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170
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<pre style="margin: 0;"> <span id="LC170" class="line" lang="diff"> }</span>
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<pre style="margin: 0;"> <span id="LC171" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- seqs = bseq_read(argv[optind], &n_seqs);</span></span>
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<pre style="margin: 0;"> <span id="LC172" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ seqs = fml_seq_read(argv[optind], &n_seqs);</span></span>
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<pre style="margin: 0;"> <span id="LC173" class="line" lang="diff"> utg = fml_assemble(&opt, n_seqs, seqs, &n_utg);</span>
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174
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<pre style="margin: 0;">-<span id="LC174" class="line" lang="diff"> fml_utg_print(n_utg, utg);</span>
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175
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<pre style="margin: 0;">-<span id="LC175" class="line" lang="diff"> <span class="idiff left right">fml_utg_destroy</span>(n_utg, utg);</span>
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="diff"> <span class="idiff left right">if (!gfa_out) </span>fml_utg_print(n_utg, utg);</span>
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175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="diff"> <span class="idiff left right">else fml_utg_print_gfa</span>(n_utg, utg);</span>
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176
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176
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<pre style="margin: 0;"> <span id="LC176" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/internal.h</span></span>
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177
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177
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<pre style="margin: 0;"> <span id="LC177" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/internal.h</span></span>
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178
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178
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<pre style="margin: 0;"> <span id="LC178" class="line" lang="diff"><span class="p">@@ -12,7 +12,7 @@</span> extern "C" {</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -189,13 +189,13 @@ Last-Update: Thu, 02 Feb 2017 10:57:56 +0100</td>
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189
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189
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<pre style="margin: 0;"> <span id="LC189" class="line" lang="diff"><span class="p">@@ -8,7 +8,7 @@</span></span>
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190
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190
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<pre style="margin: 0;"> <span id="LC190" class="line" lang="diff"> typedef struct {</span>
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191
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191
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<pre style="margin: 0;"> <span id="LC191" class="line" lang="diff"> int32_t l_seq;</span>
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192
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<pre style="margin: 0;">-<span id="LC192" class="line" lang="diff"> char *seq, *qual;</span>
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192
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="diff"> char *seq, *qual;<span class="idiff left right"> // NULL-terminated strings; length expected to match $l_seq</span></span>
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193
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193
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<pre style="margin: 0;"> <span id="LC193" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-} bseq1_t;</span></span>
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194
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<pre style="margin: 0;"> <span id="LC194" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+} fml_seq1_t;</span></span>
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195
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195
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<pre style="margin: 0;"> <span id="LC195" class="line" lang="diff"> </span>
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196
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<pre style="margin: 0;">-<span id="LC196" class="line" lang="diff"> #define MAG_F_AGGRESSIVE 0x20</span>
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197
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<pre style="margin: 0;">-<span id="LC197" class="line" lang="diff"> #define MAG_F_<span class="idiff left right">NO_SIMPL 0x80</span></span>
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198
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<pre style="margin: 0;">-<span id="LC198" class="line" lang="diff"><span class="p">@@ -6<span class="idiff left right">0,7 +60</span>,7 @@</span> extern "C" {</span>
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196
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="diff"> #define MAG_F_AGGRESSIVE 0x20<span class="idiff left right"> // pop variant bubbles (not default)</span></span>
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197
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="diff"> #define MAG_F_<span class="idiff left right">POPOPEN 0x40 // aggressive tip trimming (default)</span></span>
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198
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="diff"><span class="p">@@ -6<span class="idiff left right">3,7 +63</span>,7 @@</span> extern "C" {</span>
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199
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199
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<pre style="margin: 0;"> <span id="LC199" class="line" lang="diff"> *</span>
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200
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<pre style="margin: 0;"> <span id="LC200" class="line" lang="diff"> * @return array of sequences</span>
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201
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201
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<pre style="margin: 0;"> <span id="LC201" class="line" lang="diff"> */</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">@@ -204,7 +204,7 @@ Last-Update: Thu, 02 Feb 2017 10:57:56 +0100</td>
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204
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204
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<pre style="margin: 0;"> <span id="LC204" class="line" lang="diff"> </span>
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205
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<pre style="margin: 0;"> <span id="LC205" class="line" lang="diff"> /**</span>
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<pre style="margin: 0;"> <span id="LC206" class="line" lang="diff"> * Initialize default parameters</span>
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207
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<pre style="margin: 0;">-<span id="LC207" class="line" lang="diff"><span class="p">@@ -<span class="idiff left right">79,7 +79</span>,7 @@</span> void fml_opt_init(fml_opt_t *opt);</span>
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="diff"><span class="p">@@ -<span class="idiff left right">82,7 +82</span>,7 @@</span> void fml_opt_init(fml_opt_t *opt);</span>
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<pre style="margin: 0;"> <span id="LC208" class="line" lang="diff"> *</span>
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209
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<pre style="margin: 0;"> <span id="LC209" class="line" lang="diff"> * @return array of unitigs</span>
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<pre style="margin: 0;"> <span id="LC210" class="line" lang="diff"> */</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="213" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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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">@@ -213,7 +213,7 @@ Last-Update: Thu, 02 Feb 2017 10:57:56 +0100</td>
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<pre style="margin: 0;"> <span id="LC213" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC214" class="line" lang="diff"> /**</span>
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<pre style="margin: 0;"> <span id="LC215" class="line" lang="diff"> * Free unitigs</span>
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<pre style="margin: 0;">-<span id="LC216" class="line" lang="diff"><span class="p">@@ -10<span class="idiff left right">0,7 +100</span>,7 @@</span> void fml_utg_destroy(int n_utg, fml_utg_</span>
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="diff"><span class="p">@@ -10<span class="idiff left right">3,7 +103</span>,7 @@</span> void fml_utg_destroy(int n_utg, fml_utg_</span>
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<pre style="margin: 0;"> <span id="LC217" class="line" lang="diff"> * @param n_seqs number of sequences</span>
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<pre style="margin: 0;"> <span id="LC218" class="line" lang="diff"> * @param seqs array of sequences</span>
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<pre style="margin: 0;"> <span id="LC219" class="line" lang="diff"> */</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="222" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -222,7 +222,7 @@ Last-Update: Thu, 02 Feb 2017 10:57:56 +0100</td>
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<pre style="margin: 0;"> <span id="LC222" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC223" class="line" lang="diff"> /**</span>
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<pre style="margin: 0;"> <span id="LC224" class="line" lang="diff"> * Error correction</span>
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<pre style="margin: 0;">-<span id="LC225" class="line" lang="diff"><span class="p">@@ -11<span class="idiff left right">1,8 +111</span>,8 @@</span> void fml_opt_adjust(fml_opt_t *opt, int</span>
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="diff"><span class="p">@@ -11<span class="idiff left right">4,8 +114</span>,8 @@</span> void fml_opt_adjust(fml_opt_t *opt, int</span>
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<pre style="margin: 0;"> <span id="LC226" class="line" lang="diff"> *</span>
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<pre style="margin: 0;"> <span id="LC227" class="line" lang="diff"> * @return k-mer coverage</span>
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<pre style="margin: 0;"> <span id="LC228" class="line" lang="diff"> */</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="233" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -233,9 +233,9 @@ Last-Update: Thu, 02 Feb 2017 10:57:56 +0100</td>
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<pre style="margin: 0;"> <span id="LC233" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC234" class="line" lang="diff"> /**</span>
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<pre style="margin: 0;"> <span id="LC235" class="line" lang="diff"> * Construct FMD-index</span>
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<pre style="margin: 0;">-<span id="LC236" class="line" lang="diff"><span class="p">@@ -12<span class="idiff left right">3,7 +123</span>,7 @@</span> float fml_fltuniq(const fml_opt_t *opt,</span>
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<pre style="margin: 0;">+<span id="LC236" class="line" lang="diff"><span class="p">@@ -12<span class="idiff left right">6,7 +126</span>,7 @@</span> float fml_fltuniq(const fml_opt_t *opt,</span>
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<pre style="margin: 0;"> <span id="LC237" class="line" lang="diff"> *</span>
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<pre style="margin: 0;">-<span id="LC238" class="line" lang="diff"> * @return FMD-index</span>
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="diff"> * @return FMD-index<span class="idiff left right"> on success; NULL if all input sequences are zero in length</span></span>
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<pre style="margin: 0;"> <span id="LC239" class="line" lang="diff"> */</span>
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<pre style="margin: 0;"> <span id="LC240" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-struct rld_t *fml_seq2fmi(const fml_opt_t *opt, int n, bseq1_t *seq);</span></span>
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<pre style="margin: 0;"> <span id="LC241" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+struct rld_t *fml_seq2fmi(const fml_opt_t *opt, int n, fml_seq1_t *seq);</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">@@ -244,7 +244,7 @@ Last-Update: Thu, 02 Feb 2017 10:57:56 +0100</td>
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<pre style="margin: 0;"> <span id="LC244" class="line" lang="diff"> * Generate initial overlap graph</span>
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<pre style="margin: 0;"> <span id="LC245" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/README.md</span></span>
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<pre style="margin: 0;"> <span id="LC246" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/README.md</span></span>
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<pre style="margin: 0;">-<span id="LC247" class="line" lang="diff"><span class="p">@@ -<span class="idiff left right">29,11 +29</span>,11 @@</span> sketch of the example:</span>
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="diff"><span class="p">@@ -<span class="idiff left right">34,11 +34</span>,11 @@</span> sketch of the example:</span>
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<pre style="margin: 0;"> <span id="LC248" class="line" lang="diff"> int main(int argc, char *argv[])</span>
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<pre style="margin: 0;"> <span id="LC249" class="line" lang="diff"> {</span>
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<pre style="margin: 0;"> <span id="LC250" class="line" lang="diff"> int i, n_seqs, n_utgs;</span>
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<a href="https://salsa.debian.org/med-team/fermi-lite/-/compare/a3135da8ba6e517fb54a0f3950c62653e80783e7...24bfe49e5975666ec6bf6691c37b7ee0cc844aa1#68ef9f98c01c7eecd4c605cc26048a06f3304b79"><strong>debian/watch</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">version=3</span>
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2
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">https://github.com/lh3/fermi-lite/releases .*/archive/v(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz)</span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">version=4</span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">opts="mode=git,pretty=0.1+git%cd.%h" \</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> https://github.com/lh3/fermi-lite.git HEAD</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="LC6" class="line" lang="plaintext">#https://github.com/lh3/fermi-lite/releases .*/archive/v(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz)</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"></span></pre>
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<a href="https://salsa.debian.org/med-team/fermi-lite/-/compare/a3135da8ba6e517fb54a0f3950c62653e80783e7...24bfe49e5975666ec6bf6691c37b7ee0cc844aa1#d5b1ef39d032b550cec6ec1007b182e41ada7193"><strong>example.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">@@ -6,17 +6,21 @@</td>
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<pre style="margin: 0;"> <span id="LC6" 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="LC7" class="line" lang="c"><span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="c"> <span class="n" style="color: #333;">fml_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="LC9" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">c</span><span class="p">,</span> <span class="n" style="color: #333;">n_seqs</span><span class="p">,</span> <span class="n" style="color: #333;">n_utg</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">c</span><span class="p">,</span> <span class="n" style="color: #333;">n_seqs</span><span class="p">,</span> <span class="n" style="color: #333;">n_utg</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">gfa_out</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="LC10" class="line" lang="c"> <span class="n" style="color: #333;">bseq1_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">seqs</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="c"> <span class="n" style="color: #333;">fml_utg_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">utg</span><span class="p">;</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="n" style="color: #333;">fml_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="LC14" 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;">"<span class="idiff left right">Ae:l:r:t:c</span>:"</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="14" style="width: 35px; color: rgba(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="LC14" 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;">"<span class="idiff left right">gOAe:l:r:t:c:d:v</span>:"</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="LC15" 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;">'e'</span><span class="p">)</span> <span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">ec_k</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="LC16" 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;">'l'</span><span class="p">)</span> <span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">min_asm_ovlp</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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17
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<pre style="margin: 0;"> <span id="LC17" 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;">opt</span><span class="p">.</span><span class="n" style="color: #333;">mag_opt</span><span class="p">.</span><span class="n" style="color: #333;">min_dratio1</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="LC18" 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;">'A'</span><span class="p">)</span> <span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">mag_opt</span><span class="p">.</span><span class="n" style="color: #333;">flag</span> <span class="o" style="font-weight: 600;">|=</span> <span class="n" style="color: #333;">MAG_F_AGGRESSIVE</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC19" 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;">'O'</span><span class="p">)</span> <span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">mag_opt</span><span class="p">.</span><span class="n" style="color: #333;">flag</span> <span class="o" style="font-weight: 600;">&=</span> <span class="o" style="font-weight: 600;">~</span><span class="n" style="color: #333;">MAG_F_POPOPEN</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
20
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<pre style="margin: 0;">+<span id="LC20" 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;">'d'</span><span class="p">)</span> <span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">mag_opt</span><span class="p">.</span><span class="n" style="color: #333;">max_bdiff</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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19
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<td class="diff-line-num new_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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<pre style="margin: 0;"> <span id="LC21" 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;">'t'</span><span class="p">)</span> <span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">n_threads</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="diff-line-num new new_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
22
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<pre style="margin: 0;">+<span id="LC22" 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;">'g'</span><span class="p">)</span> <span class="n" style="color: #333;">gfa_out</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="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
23
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<pre style="margin: 0;">+<span id="LC23" 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="n" style="color: #333;">fm_verbose</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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20
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<td class="diff-line-num new_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
24
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<pre style="margin: 0;"> <span id="LC24" 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="p">{</span></span>
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21
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<td class="diff-line-num new_line" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
25
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">p</span><span class="p">;</span></span>
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22
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26
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="c"> <span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">min_cnt</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">strtol</span><span class="p">(</span><span class="n" style="color: #333;">optarg</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 class="mi" style="color: #099;">10</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="35" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -31,12 +35,16 @@ int main(int argc, char *argv[])</td>
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31
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<td class="diff-line-num new_line" data-linenumber="35" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
35
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">" -l INT min overlap length during initial assembly [%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_asm_ovlp</span><span class="p">);</span></span>
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32
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<td class="diff-line-num new_line" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
36
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">" -r FLOAT drop an overlap if its length is below maxOvlpLen*FLOAT [%g]</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;">mag_opt</span><span class="p">.</span><span class="n" style="color: #333;">min_dratio1</span><span class="p">);</span></span>
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33
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<td class="diff-line-num 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">
37
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">" -t INT number of threads (don't use multi-threading for small data sets) [%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;">n_threads</span><span class="p">);</span></span>
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34
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<td class="diff-line-num new_line old" data-linenumber="38" 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="LC34" 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;">" -A discard heterozygotes (apply this to assemble bacterial genomes)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">" -d INT retain a bubble if one side is longer than the other side by >INT-bp [%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;">mag_opt</span><span class="p">.</span><span class="n" style="color: #333;">max_bdiff</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">" -A discard heterozygotes (apply this to assemble bacterial genomes; override -O)</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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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">" -O don't apply aggressive tip trimming</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">" -g output the assembly graph in the GFA format</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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35
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<td class="diff-line-num new_line" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
42
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<pre style="margin: 0;"> <span id="LC42" 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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36
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43
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="c"> <span class="n" style="color: #333;">seqs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bseq_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="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">n_seqs</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="c"> <span class="n" style="color: #333;">utg</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fml_assemble</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;">n_seqs</span><span class="p">,</span> <span class="n" style="color: #333;">seqs</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">n_utg</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="c"> <span class="n" style="color: #333;">fml_utg_print</span><span class="p">(</span><span class="n" style="color: #333;">n_utg</span><span class="p">,</span> <span class="n" style="color: #333;">utg</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="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">gfa_out</span><span class="p">)</span> <span class="n" style="color: #333;">fml_utg_print</span><span class="p">(</span><span class="n" style="color: #333;">n_utg</span><span class="p">,</span> <span class="n" style="color: #333;">utg</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="n" style="color: #333;">fml_utg_print_gfa</span><span class="p">(</span><span class="n" style="color: #333;">n_utg</span><span class="p">,</span> <span class="n" style="color: #333;">utg</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;">fml_utg_destroy</span><span class="p">(</span><span class="n" style="color: #333;">n_utg</span><span class="p">,</span> <span class="n" style="color: #333;">utg</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">0</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></pre>
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<a href="https://salsa.debian.org/med-team/fermi-lite/-/compare/a3135da8ba6e517fb54a0f3950c62653e80783e7...24bfe49e5975666ec6bf6691c37b7ee0cc844aa1#53398c4acc0cae64b87e357193c54e2042eaa019"><strong>fml.h</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifndef FML_H</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define FML_H</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define FML_VERSION "r<span class="idiff left right">41</span>"</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define FML_VERSION "r<span class="idiff left right">55</span>"</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <stdint.h></span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="c"><span class="k" style="font-weight: 600;">typedef</span> <span class="k" style="font-weight: 600;">struct</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">l_seq</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qual</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">qual</span><span class="p">;</span><span class="idiff left"> </span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right">// NULL-terminated strings; length expected to match $l_seq</span></span></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="c"><span class="p">}</span> <span class="n" style="color: #333;">bseq1_t</span><span class="p">;</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="cp" style="color: #999; font-weight: 600;">#define MAG_F_AGGRESSIVE 0x20</span></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define MAG_F_NO_SIMPL 0x80</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define MAG_F_AGGRESSIVE 0x20 // pop variant bubbles (not default)</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define MAG_F_POPOPEN 0x40 // aggressive tip trimming (default)</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define MAG_F_NO_SIMPL 0x80 // skip bubble simplification (default)</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="k" style="font-weight: 600;">struct</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;">int</span> <span class="n" style="color: #333;">flag</span><span class="p">,</span> <span class="n" style="color: #333;">min_ovlp</span><span class="p">,</span> <span class="n" style="color: #333;">min_elen</span><span class="p">,</span> <span class="n" style="color: #333;">min_ensr</span><span class="p">,</span> <span class="n" style="color: #333;">min_insr</span><span class="p">,</span> <span class="n" style="color: #333;">max_bdist</span><span class="p">,</span> <span class="n" style="color: #333;">max_bvtx</span><span class="p">,</span> <span class="n" style="color: #333;">min_merge_len</span><span class="p">,</span> <span class="n" style="color: #333;">trim_len</span><span class="p">,</span> <span class="n" style="color: #333;">trim_depth</span><span class="p">;</span></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;">flag</span><span class="p">,</span> <span class="n" style="color: #333;">min_ovlp</span><span class="p">,</span> <span class="n" style="color: #333;">min_elen</span><span class="p">,</span> <span class="n" style="color: #333;">min_ensr</span><span class="p">,</span> <span class="n" style="color: #333;">min_insr</span><span class="p">,</span> <span class="n" style="color: #333;">max_bdist</span><span class="p">,</span> <span class="n" style="color: #333;">max_b<span class="idiff left">diff</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">max_b</span>vtx</span><span class="p">,</span> <span class="n" style="color: #333;">min_merge_len</span><span class="p">,</span> <span class="n" style="color: #333;">trim_len</span><span class="p">,</span> <span class="n" style="color: #333;">trim_depth</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;">float</span> <span class="n" style="color: #333;">min_dratio1</span><span class="p">,</span> <span class="n" style="color: #333;">max_bcov</span><span class="p">,</span> <span class="n" style="color: #333;">max_bfrac</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 class="n" style="color: #333;">magopt_t</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="c"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -31,8 +32,8 @@ struct rld_t;</td>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="c"><span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">mag_t</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="c"><span class="k" style="font-weight: 600;">typedef</span> <span class="k" style="font-weight: 600;">struct</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;"><span class="idiff left">tid</span></span><span class="p"><span class="idiff right">;</span></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;">uint32_t</span> <span class="n" style="color: #333;"><span class="idiff left">len</span></span><span class="o" style="font-weight: 600;"><span class="idiff">:</span></span><span class="mi" style="color: #099;"><span class="idiff">31</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">from</span></span><span class="o" style="font-weight: 600;"><span class="idiff">:</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff right">;</span></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;">uint32_t</span> <span class="n" style="color: #333;"><span class="idiff left">len</span></span><span class="o" style="font-weight: 600;"><span class="idiff">:</span></span><span class="mi" style="color: #099;"><span class="idiff">31</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">from</span></span><span class="o" style="font-weight: 600;"><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="idiff"> </span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right">// $from and $to: 0 meaning overlapping 5'-end; 1 overlapping 3'-end</span></span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;"><span class="idiff left">id</span></span><span class="o" style="font-weight: 600;"><span class="idiff">:</span></span><span class="mi" style="color: #099;"><span class="idiff">31</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">to</span></span><span class="o" style="font-weight: 600;"><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="idiff"> </span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right">// $id: unitig number</span></span></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="c"><span class="p">}</span> <span class="n" style="color: #333;">fml_ovlp_t</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="c"><span class="k" style="font-weight: 600;">typedef</span> <span class="k" style="font-weight: 600;">struct</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">@@ -44,6 +45,8 @@ typedef struct {</td>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="c"> <span class="n" style="color: #333;">fml_ovlp_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">ovlp</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// overlaps, of size n_ovlp[0]+n_ovlp[1]</span></span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="c"><span class="p">}</span> <span class="n" style="color: #333;">fml_utg_t</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="c"><span class="k" style="font-weight: 600;">extern</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">fm_verbose</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifdef __cplusplus</span></span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="c"><span class="k" style="font-weight: 600;">extern</span> <span class="s" style="color: #d14;">"C"</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</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">@@ -121,7 +124,7 @@ float fml_fltuniq(const fml_opt_t *opt, int n, bseq1_t *seq);</td>
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<pre style="margin: 0;"> <span id="LC124" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * @param n number of sequences</span></span>
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<pre style="margin: 0;"> <span id="LC125" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * @param seq array of sequences; FREED on return</span></span>
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<pre style="margin: 0;"> <span id="LC126" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">-<span id="LC124" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * @return FMD-index</span></span>
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * @return FMD-index<span class="idiff left right"> on success; NULL if all input sequences are zero in length</span></span></span>
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<pre style="margin: 0;"> <span id="LC128" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;"> <span id="LC129" class="line" lang="c"><span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">rld_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fml_seq2fmi</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">fml_opt_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">opt</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">n</span><span class="p">,</span> <span class="n" style="color: #333;">bseq1_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">seq</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC130" class="line" lang="c"></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="164" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -161,6 +164,14 @@ fml_utg_t *fml_mag2utg(struct mag_t *g, int *n_utg);</td>
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<pre style="margin: 0;"> <span id="LC164" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;"> <span id="LC165" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">fml_utg_print</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">n_utgs</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">fml_utg_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">utg</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC166" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * Output unitig graph in the GFA format</span></span>
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * @param n_utg number of unitigs</span></span>
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171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * @param utg array of unitigs</span></span>
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172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">fml_utg_print_gfa</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">n</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">fml_utg_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">utg</span><span class="p">);</span></span>
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174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC175" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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176
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<pre style="margin: 0;"> <span id="LC176" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * Deallocate an FM-index</span></span>
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166
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<pre style="margin: 0;"> <span id="LC177" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<a href="https://salsa.debian.org/med-team/fermi-lite/-/compare/a3135da8ba6e517fb54a0f3950c62653e80783e7...24bfe49e5975666ec6bf6691c37b7ee0cc844aa1#6bae174381d2d3da5bf4d20b215570420226d9cc"><strong>mag.c</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -28,7 +28,7 @@ KSORT_INIT_GENERIC(uint64_t)</td>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define edge_mark_del(_x) ((_x).x = (uint64_t)-2, (_x).y = 0)</span></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define edge_is_del(_x) ((_x).x == (uint64_t)-2 || (_x).y == 0)</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="c"><span class="k" style="font-weight: 600;"><span class="idiff left">static</span></span><span class="idiff right"> </span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">fm_verbose</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">fm_verbose</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/*********************</span></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * Vector operations *</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">@@ -553,6 +553,7 @@ void mag_init_opt(magopt_t *o)</td>
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<pre style="margin: 0;"> <span id="LC553" class="line" lang="c"> <span class="n" style="color: #333;">o</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">max_bfrac</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;">15</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC554" class="line" lang="c"> <span class="n" style="color: #333;">o</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">max_bvtx</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">64</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC555" class="line" lang="c"> <span class="n" style="color: #333;">o</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">max_bdist</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">512</span><span class="p">;</span></span>
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556
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<pre style="margin: 0;">+<span id="LC556" class="line" lang="c"> <span class="n" style="color: #333;">o</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">max_bdiff</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">50</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC557" class="line" lang="c"><span class="p">}</span></span>
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558
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<pre style="margin: 0;"> <span id="LC558" class="line" lang="c"></span>
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559
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<pre style="margin: 0;"> <span id="LC559" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">mag_g_clean</span><span class="p">(</span><span class="n" style="color: #333;">mag_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">g</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">magopt_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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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -568,15 +569,15 @@ void mag_g_clean(mag_t *g, const magopt_t *opt)</td>
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569
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<pre style="margin: 0;"> <span id="LC569" 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;">2</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;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">min_ensr</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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570
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<pre style="margin: 0;"> <span id="LC570" class="line" lang="c"> <span class="n" style="color: #333;">mag_g_rm_vext</span><span class="p">(</span><span class="n" style="color: #333;">g</span><span class="p">,</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">min_elen</span><span class="p">,</span> <span class="n" style="color: #333;">j</span><span class="p">);</span></span>
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570
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571
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<pre style="margin: 0;"> <span id="LC571" class="line" lang="c"> <span class="n" style="color: #333;">mag_g_merge</span><span class="p">(</span><span class="n" style="color: #333;">g</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">min_merge_len</span><span class="p">);</span></span>
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571
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<pre style="margin: 0;">-<span id="LC571" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">opt</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">flag</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">MAG_F_AGGRESSIVE</span></span><span class="p">)</span> <span class="n" style="color: #333;">mag_g_pop_open</span><span class="p">(</span><span class="n" style="color: #333;">g</span><span class="p">,</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">min_elen</span><span class="p">);</span></span>
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572
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<pre style="margin: 0;">+<span id="LC572" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(<span class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">opt</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">flag</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">MAG_F_AGGRESSIVE</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">opt</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">flag</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">MAG_F_POPOPEN</span></span><span class="p"><span class="idiff right">)</span>)</span> <span class="n" style="color: #333;">mag_g_pop_open</span><span class="p">(</span><span class="n" style="color: #333;">g</span><span class="p">,</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">min_elen</span><span class="p">);</span></span>
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573
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<pre style="margin: 0;"> <span id="LC573" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">flag</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">MAG_F_NO_SIMPL</span><span class="p">))</span> <span class="n" style="color: #333;">mag_g_simplify_bubble</span><span class="p">(</span><span class="n" style="color: #333;">g</span><span class="p">,</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">max_bvtx</span><span class="p">,</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">max_bdist</span><span class="p">);</span></span>
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573
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<pre style="margin: 0;">-<span id="LC573" class="line" lang="c"> <span class="n" style="color: #333;">mag_g_pop_simple</span><span class="p">(</span><span class="n" style="color: #333;">g</span><span class="p">,</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">max_bcov</span><span class="p">,</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">max_bfrac</span><span class="p">,</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">min_merge_len</span><span class="p">,</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">flag</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">MAG_F_AGGRESSIVE</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC574" class="line" lang="c"> <span class="n" style="color: #333;">mag_g_pop_simple</span><span class="p">(</span><span class="n" style="color: #333;">g</span><span class="p">,</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">max_bcov</span><span class="p">,</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">max_bfrac</span><span class="p">,</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">min_merge_len</span><span class="p">,</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;"><span class="idiff left">max_bdiff</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">opt</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">-></span></span><span class="n" style="color: #333;">flag</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">MAG_F_AGGRESSIVE</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC575" class="line" lang="c"> <span class="n" style="color: #333;">mag_g_rm_vint</span><span class="p">(</span><span class="n" style="color: #333;">g</span><span class="p">,</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">min_elen</span><span class="p">,</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">min_insr</span><span class="p">,</span> <span class="n" style="color: #333;">g</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">min_ovlp</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC576" class="line" lang="c"> <span class="n" style="color: #333;">mag_g_rm_edge</span><span class="p">(</span><span class="n" style="color: #333;">g</span><span class="p">,</span> <span class="n" style="color: #333;">g</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">min_ovlp</span><span class="p">,</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">min_dratio1</span><span class="p">,</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">min_elen</span><span class="p">,</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">min_ensr</span><span class="p">);</span></span>
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576
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577
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<pre style="margin: 0;"> <span id="LC577" class="line" lang="c"> <span class="n" style="color: #333;">mag_g_merge</span><span class="p">(</span><span class="n" style="color: #333;">g</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">min_merge_len</span><span class="p">);</span></span>
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577
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578
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<pre style="margin: 0;"> <span id="LC578" class="line" lang="c"> <span class="n" style="color: #333;">mag_g_rm_vext</span><span class="p">(</span><span class="n" style="color: #333;">g</span><span class="p">,</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">min_elen</span><span class="p">,</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">min_ensr</span><span class="p">);</span></span>
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578
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579
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<pre style="margin: 0;"> <span id="LC579" class="line" lang="c"> <span class="n" style="color: #333;">mag_g_merge</span><span class="p">(</span><span class="n" style="color: #333;">g</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">min_merge_len</span><span class="p">);</span></span>
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579
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<pre style="margin: 0;">-<span id="LC579" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">opt</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">flag</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">MAG_F_AGGRESSIVE</span></span><span class="p">)</span> <span class="n" style="color: #333;">mag_g_pop_open</span><span class="p">(</span><span class="n" style="color: #333;">g</span><span class="p">,</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">min_elen</span><span class="p">);</span></span>
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580
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<pre style="margin: 0;">+<span id="LC580" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(<span class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">opt</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">flag</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">MAG_F_AGGRESSIVE</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">opt</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">flag</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">MAG_F_POPOPEN</span></span><span class="p"><span class="idiff right">)</span>)</span> <span class="n" style="color: #333;">mag_g_pop_open</span><span class="p">(</span><span class="n" style="color: #333;">g</span><span class="p">,</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">min_elen</span><span class="p">);</span></span>
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581
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<pre style="margin: 0;"> <span id="LC581" class="line" lang="c"> <span class="n" style="color: #333;">mag_g_rm_vext</span><span class="p">(</span><span class="n" style="color: #333;">g</span><span class="p">,</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">min_elen</span><span class="p">,</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">min_ensr</span><span class="p">);</span></span>
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581
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582
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<pre style="margin: 0;"> <span id="LC582" class="line" lang="c"> <span class="n" style="color: #333;">mag_g_merge</span><span class="p">(</span><span class="n" style="color: #333;">g</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">min_merge_len</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC583" class="line" lang="c"><span class="p">}</span></span>
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<a href="https://salsa.debian.org/med-team/fermi-lite/-/compare/a3135da8ba6e517fb54a0f3950c62653e80783e7...24bfe49e5975666ec6bf6691c37b7ee0cc844aa1#276dcdf4b383e79a86bb74ce20195cee3a958ae8"><strong>mag.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">@@ -49,7 +49,7 @@ extern "C" {</td>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">mag_g_rm_edge</span><span class="p">(</span><span class="n" style="color: #333;">mag_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">g</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;">double</span> <span class="n" style="color: #333;">min_ratio</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">min_len</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">min_nsr</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">mag_g_merge</span><span class="p">(</span><span class="n" style="color: #333;">mag_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">g</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">rmdup</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">min_merge_len</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;">void</span> <span class="n" style="color: #333;">mag_g_simplify_bubble</span><span class="p">(</span><span class="n" style="color: #333;">mag_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">g</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">max_vtx</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">max_dist</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">mag_g_pop_simple</span><span class="p">(</span><span class="n" style="color: #333;">mag_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">g</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">max_cov</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">max_frac</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">min_merge_len</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">aggressive</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">mag_g_pop_simple</span><span class="p">(</span><span class="n" style="color: #333;">mag_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">g</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">max_cov</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">max_frac</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">min_merge_len</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;"><span class="idiff left">max_bdiff</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">int</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">aggressive</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">mag_g_pop_open</span><span class="p">(</span><span class="n" style="color: #333;">mag_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">g</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">min_elen</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">mag_g_trim_open</span><span class="p">(</span><span class="n" style="color: #333;">mag_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">g</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">magopt_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="LC55" class="line" lang="c"></span>
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<a href="https://salsa.debian.org/med-team/fermi-lite/-/compare/a3135da8ba6e517fb54a0f3950c62653e80783e7...24bfe49e5975666ec6bf6691c37b7ee0cc844aa1#c6126a1e83607d3fdd02ded564d99e9f160cf712"><strong>misc.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">@@ -37,7 +37,7 @@ void fml_opt_init(fml_opt_t *opt)</td>
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<pre style="margin: 0;"> <span id="LC37" 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_asm_ovlp</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">33</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;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">min_merge_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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<pre style="margin: 0;"> <span id="LC39" class="line" lang="c"> <span class="n" style="color: #333;">mag_init_opt</span><span class="p">(</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;">mag_opt</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="c"> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">mag_opt</span><span class="p">.</span><span class="n" style="color: #333;">flag</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">MAG_F_NO_SIMPL</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="c"> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">mag_opt</span><span class="p">.</span><span class="n" style="color: #333;">flag</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">MAG_F_NO_SIMPL</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">|</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">MAG_F_POPOPEN</span></span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="c"><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="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">fml_opt_adjust</span><span class="p">(</span><span class="n" style="color: #333;">fml_opt_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">opt</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">n_seqs</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">bseq1_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">seqs</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">@@ -72,6 +72,11 @@ struct rld_t *fml_fmi_gen(int n, bseq1_t *seq, int is_mt)</td>
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="c"> <span class="n" style="color: #333;">rld_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">e</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">k</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">k</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;">k</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;">k</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">seq</span><span class="p">[</span><span class="n" style="color: #333;">k</span><span class="p">].</span><span class="n" style="color: #333;">l_seq</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="c"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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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="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">n</span><span class="p">)</span> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="c"></span>
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75
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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;">mr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mr_init</span><span class="p">(</span><span class="n" style="color: #333;">ROPE_DEF_MAX_NODES</span><span class="p">,</span> <span class="n" style="color: #333;">ROPE_DEF_BLOCK_LEN</span><span class="p">,</span> <span class="n" style="color: #333;">MR_SO_RCLO</span><span class="p">);</span></span>
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76
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81
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">k</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;">k</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;">k</span><span class="p">)</span> <span class="p">{</span></span>
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77
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82
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="198" style="width: 35px; color: rgba(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">@@ -193,7 +198,8 @@ fml_utg_t *fml_mag2utg(struct mag_t *g, int *n)</td>
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193
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198
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<pre style="margin: 0;"> <span id="LC198" class="line" lang="c"> <span class="n" style="color: #333;">t</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">q</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">ovlp</span><span class="p">[</span><span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">++</span><span class="p">];</span></span>
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194
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199
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<pre style="margin: 0;"> <span id="LC199" class="line" lang="c"> <span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kh_get</span><span class="p">(</span><span class="mi" style="color: #099;">64</span><span class="p">,</span> <span class="n" style="color: #333;">h</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;">x</span><span class="p">);</span></span>
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195
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200
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<pre style="margin: 0;"> <span id="LC200" class="line" lang="c"> <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">kh_end</span><span class="p">(</span><span class="n" style="color: #333;">h</span><span class="p">));</span></span>
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196
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<pre style="margin: 0;">-<span id="LC196" class="line" lang="c"> <span class="n" style="color: #333;">t</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">tid</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kh_val</span><span class="p">(</span><span class="n" style="color: #333;">h</span><span class="p">,</span> <span class="n" style="color: #333;">k</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="201" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
201
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="c"> <span class="n" style="color: #333;">t</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">id</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kh_val</span><span class="p">(</span><span class="n" style="color: #333;">h</span><span class="p">,</span> <span class="n" style="color: #333;">k</span><span class="p">)</span> <span class="o" style="font-weight: 600;">>></span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="202" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
202
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="c"> <span class="n" style="color: #333;">t</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">to</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kh_val</span><span class="p">(</span><span class="n" style="color: #333;">h</span><span class="p">,</span> <span class="n" style="color: #333;">k</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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197
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203
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<pre style="margin: 0;"> <span id="LC203" class="line" lang="c"> <span class="n" style="color: #333;">t</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">y</span><span class="p">;</span></span>
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198
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204
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<pre style="margin: 0;"> <span id="LC204" class="line" lang="c"> <span class="n" style="color: #333;">t</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">from</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">from</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="199" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
199
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<td class="diff-line-num new_line" data-linenumber="205" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
205
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<pre style="margin: 0;"> <span id="LC205" 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="217" style="width: 35px; color: rgba(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="223" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -217,13 +223,13 @@ void fml_utg_print(int n, const fml_utg_t *utg)</td>
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217
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223
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<pre style="margin: 0;"> <span id="LC223" class="line" lang="c"> <span class="n" style="color: #333;">kputc</span><span class="p">(</span><span class="sc" style="color: #d14;">'\t'</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">out</span><span class="p">);</span> <span class="n" style="color: #333;">kputw</span><span class="p">(</span><span class="n" style="color: #333;">u</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">nsr</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">out</span><span class="p">);</span></span>
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218
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224
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<pre style="margin: 0;"> <span id="LC224" class="line" lang="c"> <span class="n" style="color: #333;">kputc</span><span class="p">(</span><span class="sc" style="color: #d14;">'\t'</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">out</span><span class="p">);</span></span>
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219
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225
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<pre style="margin: 0;"> <span id="LC225" 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;">u</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">n_ovlp</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;">j</span><span class="p">)</span> <span class="p">{</span></span>
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220
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<pre style="margin: 0;">-<span id="LC220" class="line" lang="c"> <span class="n" style="color: #333;">kputw</span><span class="p">(</span><span class="n" style="color: #333;">u</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">ovlp</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">].</span><span class="n" style="color: #333;"><span class="idiff left right">tid</span></span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">out</span><span class="p">);</span> <span class="n" style="color: #333;">kputc</span><span class="p">(</span><span class="sc" style="color: #d14;">','</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">out</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="c"> <span class="n" style="color: #333;">kputw</span><span class="p">(</span><span class="n" style="color: #333;">u</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">ovlp</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">].</span><span class="n" style="color: #333;"><span class="idiff left">id</span></span><span class="o" style="font-weight: 600;"><span class="idiff"><<</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="o" style="font-weight: 600;"><span class="idiff">|</span></span><span class="n" style="color: #333;"><span class="idiff">u</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">ovlp</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">j</span></span><span class="p"><span class="idiff">].</span></span><span class="n" style="color: #333;"><span class="idiff right">to</span></span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">out</span><span class="p">);</span> <span class="n" style="color: #333;">kputc</span><span class="p">(</span><span class="sc" style="color: #d14;">','</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">out</span><span class="p">);</span></span>
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227
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<pre style="margin: 0;"> <span id="LC227" class="line" lang="c"> <span class="n" style="color: #333;">kputw</span><span class="p">(</span><span class="n" style="color: #333;">u</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">ovlp</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">].</span><span class="n" style="color: #333;">len</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">out</span><span class="p">);</span> <span class="n" style="color: #333;">kputc</span><span class="p">(</span><span class="sc" style="color: #d14;">';'</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">out</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC228" class="line" lang="c"> <span class="p">}</span></span>
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229
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<pre style="margin: 0;"> <span id="LC229" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">u</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">n_ovlp</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 class="n" style="color: #333;">kputc</span><span class="p">(</span><span class="sc" style="color: #d14;">'.'</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">out</span><span class="p">);</span></span>
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230
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<pre style="margin: 0;"> <span id="LC230" class="line" lang="c"> <span class="n" style="color: #333;">kputc</span><span class="p">(</span><span class="sc" style="color: #d14;">'\t'</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">out</span><span class="p">);</span></span>
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231
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<pre style="margin: 0;"> <span id="LC231" 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="n" style="color: #333;">u</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">n_ovlp</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;">u</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">n_ovlp</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;">j</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC226" class="line" lang="c"> <span class="n" style="color: #333;">kputw</span><span class="p">(</span><span class="n" style="color: #333;">u</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">ovlp</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">].</span><span class="n" style="color: #333;"><span class="idiff left right">tid</span></span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">out</span><span class="p">);</span> <span class="n" style="color: #333;">kputc</span><span class="p">(</span><span class="sc" style="color: #d14;">','</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">out</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC232" class="line" lang="c"> <span class="n" style="color: #333;">kputw</span><span class="p">(</span><span class="n" style="color: #333;">u</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">ovlp</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">].</span><span class="n" style="color: #333;"><span class="idiff left">id</span></span><span class="o" style="font-weight: 600;"><span class="idiff"><<</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="o" style="font-weight: 600;"><span class="idiff">|</span></span><span class="n" style="color: #333;"><span class="idiff">u</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">ovlp</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">j</span></span><span class="p"><span class="idiff">].</span></span><span class="n" style="color: #333;"><span class="idiff right">to</span></span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">out</span><span class="p">);</span> <span class="n" style="color: #333;">kputc</span><span class="p">(</span><span class="sc" style="color: #d14;">','</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">out</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC233" class="line" lang="c"> <span class="n" style="color: #333;">kputw</span><span class="p">(</span><span class="n" style="color: #333;">u</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">ovlp</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">].</span><span class="n" style="color: #333;">len</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">out</span><span class="p">);</span> <span class="n" style="color: #333;">kputc</span><span class="p">(</span><span class="sc" style="color: #d14;">';'</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">out</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC234" class="line" lang="c"> <span class="p">}</span></span>
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235
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<pre style="margin: 0;"> <span id="LC235" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">u</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">n_ovlp</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;">0</span><span class="p">)</span> <span class="n" style="color: #333;">kputc</span><span class="p">(</span><span class="sc" style="color: #d14;">'.'</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">out</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="238" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="244" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -238,6 +244,26 @@ void fml_utg_print(int n, const fml_utg_t *utg)</td>
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<pre style="margin: 0;"> <span id="LC244" class="line" lang="c"> <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">.</span><span class="n" style="color: #333;">s</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC245" class="line" lang="c"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC246" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">fml_utg_print_gfa</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">n</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">fml_utg_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">utg</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC248" class="line" lang="c"><span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC249" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">j</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="250" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
250
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<pre style="margin: 0;">+<span id="LC250" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">stdout</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="251" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
251
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<pre style="margin: 0;">+<span id="LC251" class="line" lang="c"> <span class="n" style="color: #333;">fputs</span><span class="p">(</span><span class="s" style="color: #d14;">"H</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">VN:Z:1.0</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;">fp</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="252" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
252
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<pre style="margin: 0;">+<span id="LC252" 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;">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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<td class="diff-line-num new new_line" data-linenumber="253" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
253
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<pre style="margin: 0;">+<span id="LC253" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">fml_utg_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">u</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">utg</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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<td class="diff-line-num new new_line" data-linenumber="254" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
254
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<pre style="margin: 0;">+<span id="LC254" 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;">"S</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%d</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">i</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="255" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
255
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<pre style="margin: 0;">+<span id="LC255" class="line" lang="c"> <span class="n" style="color: #333;">fputs</span><span class="p">(</span><span class="n" style="color: #333;">u</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;">fp</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="256" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
256
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<pre style="margin: 0;">+<span id="LC256" 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;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">LN:i:%d</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">RC:i:%d</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">PD:Z:"</span><span class="p">,</span> <span class="n" style="color: #333;">u</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">len</span><span class="p">,</span> <span class="n" style="color: #333;">u</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">nsr</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="257" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
257
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<pre style="margin: 0;">+<span id="LC257" class="line" lang="c"> <span class="n" style="color: #333;">fputs</span><span class="p">(</span><span class="n" style="color: #333;">u</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">cov</span><span class="p">,</span> <span class="n" style="color: #333;">fp</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="258" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
258
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<pre style="margin: 0;">+<span id="LC258" class="line" lang="c"> <span class="n" style="color: #333;">fputc</span><span class="p">(</span><span class="sc" style="color: #d14;">'\n'</span><span class="p">,</span> <span class="n" style="color: #333;">fp</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="259" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
259
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<pre style="margin: 0;">+<span id="LC259" 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;">u</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">n_ovlp</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;">u</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">n_ovlp</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;">j</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="260" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
260
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<pre style="margin: 0;">+<span id="LC260" class="line" lang="c"> <span class="n" style="color: #333;">fml_ovlp_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">o</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">u</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">ovlp</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">];</span></span>
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<td class="diff-line-num new new_line" data-linenumber="261" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
261
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<pre style="margin: 0;">+<span id="LC261" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">o</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">id</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="262" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
262
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<pre style="margin: 0;">+<span id="LC262" 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;">%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><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;">%dM</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;">i</span><span class="p">,</span> <span class="s" style="color: #d14;">"+-"</span><span class="p">[</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">o</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">from</span><span class="p">],</span> <span class="n" style="color: #333;">o</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">id</span><span class="p">,</span> <span class="s" style="color: #d14;">"+-"</span><span class="p">[</span><span class="n" style="color: #333;">o</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">to</span><span class="p">],</span> <span class="n" style="color: #333;">o</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">len</span><span class="p">);</span></span>
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263
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<pre style="margin: 0;">+<span id="LC263" class="line" lang="c"> <span class="p">}</span></span>
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264
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<pre style="margin: 0;">+<span id="LC264" class="line" lang="c"> <span class="p">}</span></span>
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265
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<pre style="margin: 0;">+<span id="LC265" class="line" lang="c"><span class="p">}</span></span>
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266
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<pre style="margin: 0;">+<span id="LC266" class="line" lang="c"></span>
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241
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267
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<pre style="margin: 0;"> <span id="LC267" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">fml_utg_destroy</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">n</span><span class="p">,</span> <span class="n" style="color: #333;">fml_utg_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">utg</span><span class="p">)</span></span>
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268
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<pre style="margin: 0;"> <span id="LC268" class="line" lang="c"><span class="p">{</span></span>
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243
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269
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<pre style="margin: 0;"> <span id="LC269" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="259" style="width: 35px; color: rgba(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="285" style="width: 35px; color: rgba(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">@@ -259,10 +285,12 @@ fml_utg_t *fml_assemble(const fml_opt_t *opt0, int n_seqs, bseq1_t *seqs, int *n</td>
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259
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<td class="diff-line-num new_line" data-linenumber="285" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
285
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<pre style="margin: 0;"> <span id="LC285" class="line" lang="c"> <span class="n" style="color: #333;">fml_opt_t</span> <span class="n" style="color: #333;">opt</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">opt0</span><span class="p">;</span></span>
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260
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<td class="diff-line-num new_line" data-linenumber="286" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
286
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<pre style="margin: 0;"> <span id="LC286" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">kcov</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="261" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
261
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<td class="diff-line-num new_line" data-linenumber="287" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
287
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<pre style="margin: 0;"> <span id="LC287" class="line" lang="c"></span>
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<td class="diff-line-num new new_line" data-linenumber="288" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
288
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<pre style="margin: 0;">+<span id="LC288" class="line" lang="c"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">n_utg</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="262" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
262
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<td class="diff-line-num new_line" data-linenumber="289" style="width: 35px; color: rgba(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="LC289" class="line" lang="c"> <span class="n" style="color: #333;">fml_opt_adjust</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;">n_seqs</span><span class="p">,</span> <span class="n" style="color: #333;">seqs</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="263" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
263
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<td class="diff-line-num new_line" data-linenumber="290" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
290
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<pre style="margin: 0;"> <span id="LC290" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">ec_k</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;">fml_correct</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;">n_seqs</span><span class="p">,</span> <span class="n" style="color: #333;">seqs</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="264" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
264
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<td class="diff-line-num new_line" data-linenumber="291" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
291
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<pre style="margin: 0;"> <span id="LC291" class="line" lang="c"> <span class="n" style="color: #333;">kcov</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fml_fltuniq</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;">n_seqs</span><span class="p">,</span> <span class="n" style="color: #333;">seqs</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="265" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
265
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<td class="diff-line-num new_line" data-linenumber="292" style="width: 35px; color: rgba(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="LC292" class="line" lang="c"> <span class="n" style="color: #333;">e</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fml_seq2fmi</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;">n_seqs</span><span class="p">,</span> <span class="n" style="color: #333;">seqs</span><span class="p">);</span></span>
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<td class="diff-line-num new old_line" data-linenumber="266" style="width: 35px; color: rgba(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="293" style="width: 35px; color: rgba(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="LC293" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">e</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;">return</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// this may happen when all sequences are filtered out</span></span>
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266
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<td class="diff-line-num new_line" data-linenumber="294" style="width: 35px; color: rgba(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="LC294" class="line" lang="c"> <span class="n" style="color: #333;">g</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fml_fmi2mag</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;">e</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="267" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
267
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<td class="diff-line-num new_line" data-linenumber="295" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
295
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<pre style="margin: 0;"> <span id="LC295" class="line" lang="c"> <span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">mag_opt</span><span class="p">.</span><span class="n" style="color: #333;">min_ensr</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;">mag_opt</span><span class="p">.</span><span class="n" style="color: #333;">min_ensr</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">kcov</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">MAG_MIN_NSR_COEF</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;">mag_opt</span><span class="p">.</span><span class="n" style="color: #333;">min_ensr</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;">kcov</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">MAG_MIN_NSR_COEF</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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<td class="diff-line-num old_line" data-linenumber="268" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
268
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<td class="diff-line-num new_line" data-linenumber="296" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
296
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<pre style="margin: 0;"> <span id="LC296" class="line" lang="c"> <span class="n" style="color: #333;">opt</span><span class="p">.</span><span class="n" style="color: #333;">mag_opt</span><span class="p">.</span><span class="n" style="color: #333;">min_ensr</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;">mag_opt</span><span class="p">.</span><span class="n" style="color: #333;">min_ensr</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">opt0</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">max_cnt</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;">mag_opt</span><span class="p">.</span><span class="n" style="color: #333;">min_ensr</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">opt0</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">max_cnt</span><span class="p">;</span></span>
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