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<h3>
Michael R. Crusoe pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/gffread">Debian Med / gffread</a>
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<h4>
Commits:
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<ul>
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<strong><a href="https://salsa.debian.org/med-team/gffread/-/commit/f766babe0952b275c0c222adb97e89c40e3f1ac9">f766babe</a></strong>
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<span>by Michael R. Crusoe</span>
<i>at 2020-04-03T11:13:41+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 0.11.8</pre>
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<h4>5 changed files:</h4>
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<a href="#0398ccd0f49298b10a3d76a47800d2ebecd49859">
LICENSE
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<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
README.md
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<a href="#2e62d67be9b972fb94be4079924f65c3df9a24ac">
gff_utils.cpp
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<a href="#70793cbfea41a48621c826d9f427c35d8ef91e5f">
gff_utils.h
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<a href="#037bd3173d312d85c9ae5e3fa8f48a79706aa6fb">
gffread.cpp
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<h4>Changes:</h4>
<li id="0398ccd0f49298b10a3d76a47800d2ebecd49859">
<a href="https://salsa.debian.org/med-team/gffread/-/commit/f766babe0952b275c0c222adb97e89c40e3f1ac9#0398ccd0f49298b10a3d76a47800d2ebecd49859"><strong>LICENSE</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">MIT License</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">Copyright (c) 2001<span class="idiff left right">-2018</span> Geo Pertea</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">Copyright (c) 2001 Geo Pertea</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Permission is hereby granted, free of charge, to any person obtaining a copy</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">of this software and associated documentation files (the "Software"), to deal</span>
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<li id="8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
<a href="https://salsa.debian.org/med-team/gffread/-/commit/f766babe0952b275c0c222adb97e89c40e3f1ac9#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d"><strong>README.md</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2,11 +2,10 @@</td>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="markdown">GFF/GTF parsing utility providing format conversions, region filtering, </span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="markdown">FASTA sequence extraction and more.</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="markdown">Use gffread -h to check the usage options.</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="markdown">Compiling this program from source requires <span class="idiff left right">my other</span> code </span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="markdown">library<span class="idiff left">, </span><span class="p"><span class="idiff">[</span></span><span class="nv" style="color: #008080;"><span class="idiff">GCLib</span></span><span class="p"><span class="idiff">](</span></span><span class="sx" style="color: #d14;"><span class="idiff">../../../gclib</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff right">. It</span> can be done like this:</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="markdown">Compiling this program from source requires <span class="idiff left">the </span><span class="p"><span class="idiff">[</span></span><span class="nv" style="color: #008080;"><span class="idiff">GCLib</span></span><span class="p"><span class="idiff">](</span></span><span class="sx" style="color: #d14;"><span class="idiff">../../../gclib</span></span><span class="p"><span class="idiff right">)</span></span> code </span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="markdown">library<span class="idiff left right">. Building the program</span> can be done like this:</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="markdown"> cd /some/build/dir</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="15" style="width: 35px; color: rgba(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="14" style="width: 35px; color: rgba(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">@@ -15,4 +14,5 @@ library, [GCLib](../../../gclib). It can be done like this:</td>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="markdown"> cd gffread</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="markdown"> make release</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="markdown">This should build the <span class="gs" style="font-weight: 600;">**gffread**</span> binary in the current directory.</span></pre>
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<li id="2e62d67be9b972fb94be4079924f65c3df9a24ac">
<a href="https://salsa.debian.org/med-team/gffread/-/commit/f766babe0952b275c0c222adb97e89c40e3f1ac9#2e62d67be9b972fb94be4079924f65c3df9a24ac"><strong>gff_utils.cpp</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2,38 +2,12 @@</td>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">verbose</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">false</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">//same with GffReader::showWarnings and GffLoader::beVserbose</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//bool debugState=false;</span></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/*</span></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">void printTabFormat(FILE* f, GffObj* t) {</span></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> static char dbuf[1024];</span></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> fprintf(f, "%s\t%s\t%c\t%d\t%d\t%d\t", t->getID(), t->getGSeqName(), t->strand, t->start, t->end, t->exons.Count());</span></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> t->printExonList(f);</span></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> if (t->hasCDS()) fprintf(f, "\t%d:%d", t->CDstart, t->CDend);</span></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> else fprintf(f, "\t.");</span></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> if (t->getGeneID()!=NULL)</span></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> fprintf(f, "\tgeneID=%s",t->getGeneID());</span></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> if (t->getGeneName()!=NULL) {</span></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> GffObj::decodeHexChars(dbuf, t->getGeneName());</span></span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> fprintf(f, "\tgene_name=%s", dbuf);</span></span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="cpp"><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="cpp"><span class="cm" style="color: #998; font-style: italic;"> if (t->attrs!=NULL) {</span></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> for (int i=0;i<t->attrs->Count();i++) {</span></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> const char* attrname=t->getAttrName(i);</span></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> GffObj::decodeHexChars(dbuf, t->attrs->Get(i)->attr_val);</span></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> fprintf(f,"\t%s=%s", attrname, dbuf);</span></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> }</span></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> }</span></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> fprintf(f, "\n");</span></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">}</span></span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">*/</span></span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">printFasta</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">FILE</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">f</span><span class="p">,</span> <span class="n" style="color: #333;">GStr</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">defline</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;">seq</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">seqlen</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">useStar</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">printFasta</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">FILE</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">f</span><span class="p">,</span> <span class="n" style="color: #333;">GStr</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">defline</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;">seq</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">seqlen</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">useStar</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">seq</span><span class="o" style="font-weight: 600;">==</span><span class="nb" style="color: #0086b3;">NULL</span><span class="p">)</span> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">len</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="n" style="color: #333;">seqlen</span><span class="o" style="font-weight: 600;">></span><span class="mi" style="color: #099;">0</span><span class="p">)</span><span class="o" style="font-weight: 600;">?</span><span class="n" style="color: #333;">seqlen</span><span class="o" style="font-weight: 600;">:</span><span class="n" style="color: #333;">strlen</span><span class="p">(</span><span class="n" style="color: #333;">seq</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">len</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="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;"><span class="idiff left">!</span></span><span class="n" style="color: #333;"><span class="idiff">defline</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">is_empty</span></span><span class="p"><span class="idiff right">()</span>)</span></span>
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36
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">,</span> <span class="s" style="color: #d14;">">%s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">defline</span><span class="p"><span class="idiff left right">.</span></span><span class="n" style="color: #333;">chars</span><span class="p">());</span></span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">defline</span></span><span class="o" style="font-weight: 600;"><span class="idiff">!=</span></span><span class="nb" style="color: #0086b3;"><span class="idiff right">NULL</span></span><span class="p">)</span></span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">,</span> <span class="s" style="color: #d14;">">%s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">defline</span><span class="o" style="font-weight: 600;"><span class="idiff left right">-></span></span><span class="n" style="color: #333;">chars</span><span class="p">());</span></span>
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11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ilen</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="LC12" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</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;">len</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">,</span> <span class="n" style="color: #333;">ilen</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">ilen</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">70</span><span class="p">)</span> <span class="p">{</span></span>
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<a href="https://salsa.debian.org/med-team/gffread/-/commit/f766babe0952b275c0c222adb97e89c40e3f1ac9#70793cbfea41a48621c826d9f427c35d8ef91e5f"><strong>gff_utils.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">@@ -627,7 +627,7 @@ class GffLoader {</td>
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<pre style="margin: 0;"> <span id="LC627" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC628" class="line" lang="cpp"><span class="p">};</span></span>
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<pre style="margin: 0;"> <span id="LC629" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC630" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">printFasta</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">FILE</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">f</span><span class="p">,</span> <span class="n" style="color: #333;">GStr</span><span class="o" style="font-weight: 600;"><span class="idiff left right">&</span></span> <span class="n" style="color: #333;">defline</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;">seq</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">seqlen</span><span class="o" style="font-weight: 600;">=-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">useStar</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">false</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC630" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">printFasta</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">FILE</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">f</span><span class="p">,</span> <span class="n" style="color: #333;">GStr</span><span class="o" style="font-weight: 600;"><span class="idiff left right">*</span></span> <span class="n" style="color: #333;">defline</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;">seq</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">seqlen</span><span class="o" style="font-weight: 600;">=-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">useStar</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">false</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC631" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC632" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//void printTabFormat(FILE* f, GffObj* t);</span></span>
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<pre style="margin: 0;"> <span id="LC633" class="line" lang="cpp"></span>
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<a href="https://salsa.debian.org/med-team/gffread/-/commit/f766babe0952b275c0c222adb97e89c40e3f1ac9#037bd3173d312d85c9ae5e3fa8f48a79706aa6fb"><strong>gffread.cpp</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">@@ -4,7 +4,7 @@</td>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#define __STDC_FORMAT_MACROS</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <inttypes.h></span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#define VERSION "0.11.<span class="idiff left right">7</span>"</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#define VERSION "0.11.<span class="idiff left right">8</span>"</span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#define USAGE "gffread v" VERSION ". Usage:\n\</span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">gffread <input_gff> [-g <genomic_seqs_fasta> | <dir>][-s <seq_info.fsize>] \n\</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">@@ -105,9 +105,8 @@ Output options:\n\</td>
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<pre style="margin: 0;"> <span id="LC105" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"> both upstream and downstream of the transcript boundaries\n\</span></span>
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<pre style="margin: 0;"> <span id="LC106" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"> -x write a fasta file with spliced CDS for each GFF transcript\n\</span></span>
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<pre style="margin: 0;"> <span id="LC107" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"> -y write a protein fasta file with the translation of CDS for each record\n\</span></span>
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<pre style="margin: 0;">-<span id="LC108" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"> -W for -w and -x options, write in the FASTA defline the exon\n\</span></span>
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"> -W for -w and -x options, write in the FASTA defline <span class="idiff left right">all </span>the exon\n\</span></span>
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<pre style="margin: 0;"> <span id="LC109" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"> coordinates projected onto the spliced sequence;\n\</span></span>
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<pre style="margin: 0;">-<span id="LC110" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"> for -y option, write transcript attributes in the FASTA defline\n\</span></span>
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<pre style="margin: 0;"> <span id="LC110" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"> -S for -y option, use '*' instead of '.' as stop codon translation\n\</span></span>
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<pre style="margin: 0;"> <span id="LC111" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"> -L Ensembl GTF to GFF3 conversion (implies -F; should be used with -m)\n\</span></span>
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<pre style="margin: 0;"> <span id="LC112" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"> -m <chr_replace> is a name mapping table for converting reference \n\</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -128,6 +127,9 @@ Output options:\n\</td>
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<pre style="margin: 0;"> <span id="LC127" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"> pseudo-attributes (prefixed by @) are recognized:\n\</span></span>
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<pre style="margin: 0;"> <span id="LC128" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"> @id, @geneid, @chr, @start, @end, @strand, @numexons, @exons, \n\</span></span>
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<pre style="margin: 0;"> <span id="LC129" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"> @cds, @covlen, @cdslen\n\</span></span>
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"> If any of -w/-y/-x FASTA output files are enabled, the same fields\n\</span></span>
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"> (excluding @id) are appended to the definition line of corresponding\n\</span></span>
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"> FASTA records\n\</span></span>
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<pre style="margin: 0;"> <span id="LC133" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"> -v,-E expose (warn about) duplicate transcript IDs and other potential\n\</span></span>
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<pre style="margin: 0;"> <span id="LC134" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"> problems with the given GFF/GTF records\n\</span></span>
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<pre style="margin: 0;"> <span id="LC135" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">"</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="163" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -161,7 +163,8 @@ class RefTran {</td>
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<pre style="margin: 0;"> <span id="LC163" class="line" lang="cpp"><span class="k" style="font-weight: 600;">enum</span> <span class="n" style="color: #333;">ETableFieldType</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC164" class="line" lang="cpp"> <span class="n" style="color: #333;">ctfGFF_Attr</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="c1" style="color: #998; font-style: italic;">// attribute name as is</span></span>
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<pre style="margin: 0;"> <span id="LC165" class="line" lang="cpp"> <span class="n" style="color: #333;">ctfGFF_ID</span><span class="p">,</span> <span class="c1" style="color: #998; font-style: italic;">//ID or @id or transcript_id</span></span>
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164
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<pre style="margin: 0;">-<span id="LC164" class="line" lang="cpp"> <span class="n" style="color: #333;">ctfGFF_geneID</span><span class="p">,</span> <span class="c1" style="color: #998; font-style: italic;">//geneID or @gene_id</span></span>
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<td class="diff-line-num new old_line" data-linenumber="165" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="cpp"> <span class="n" style="color: #333;">ctfGFF_geneID</span><span class="p">,</span> <span class="c1" style="color: #998; font-style: italic;">//geneID or @gene_id or @geneid</span></span>
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<td class="diff-line-num new new_line" data-linenumber="167" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="cpp"> <span class="n" style="color: #333;">ctfGFF_geneName</span><span class="p">,</span> <span class="c1" style="color: #998; font-style: italic;">//geneName or @gene_name or @genename</span></span>
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<td class="diff-line-num old_line" data-linenumber="165" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
165
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<td class="diff-line-num new_line" data-linenumber="168" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
168
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<pre style="margin: 0;"> <span id="LC168" class="line" lang="cpp"> <span class="n" style="color: #333;">ctfGFF_Parent</span><span class="p">,</span> <span class="c1" style="color: #998; font-style: italic;">//Parent or @parent</span></span>
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<td class="diff-line-num old_line" data-linenumber="166" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
166
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<td class="diff-line-num new_line" data-linenumber="169" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
169
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<pre style="margin: 0;"> <span id="LC169" class="line" lang="cpp"> <span class="n" style="color: #333;">ctfGFF_chr</span><span class="p">,</span> <span class="c1" style="color: #998; font-style: italic;">//@chr</span></span>
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<td class="diff-line-num old_line" data-linenumber="167" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
167
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<td class="diff-line-num new_line" data-linenumber="170" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
170
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<pre style="margin: 0;"> <span id="LC170" class="line" lang="cpp"> <span class="n" style="color: #333;">ctfGFF_feature</span><span class="p">,</span> <span class="c1" style="color: #998; font-style: italic;">//@feature</span></span>
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<td class="diff-line-num unfold js-unfold old_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">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="299" style="width: 35px; color: rgba(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">@@ -296,6 +299,7 @@ void setTableFormat(GStr& s) {</td>
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296
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<td class="diff-line-num new_line" data-linenumber="299" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
299
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<pre style="margin: 0;"> <span id="LC299" class="line" lang="cpp"> <span class="n" style="color: #333;">specialFields</span><span class="p">.</span><span class="n" style="color: #333;">Add</span><span class="p">(</span><span class="s" style="color: #d14;">"chr"</span><span class="p">,</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">ETableFieldType</span><span class="p">(</span><span class="n" style="color: #333;">ctfGFF_chr</span><span class="p">));</span></span>
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<td class="diff-line-num old_line" data-linenumber="297" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
297
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<td class="diff-line-num new_line" data-linenumber="300" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
300
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<pre style="margin: 0;"> <span id="LC300" class="line" lang="cpp"> <span class="n" style="color: #333;">specialFields</span><span class="p">.</span><span class="n" style="color: #333;">Add</span><span class="p">(</span><span class="s" style="color: #d14;">"id"</span><span class="p">,</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">ETableFieldType</span><span class="p">(</span><span class="n" style="color: #333;">ctfGFF_ID</span><span class="p">));</span></span>
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<td class="diff-line-num old_line" data-linenumber="298" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
298
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<td class="diff-line-num new_line" data-linenumber="301" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
301
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<pre style="margin: 0;"> <span id="LC301" class="line" lang="cpp"> <span class="n" style="color: #333;">specialFields</span><span class="p">.</span><span class="n" style="color: #333;">Add</span><span class="p">(</span><span class="s" style="color: #d14;">"geneid"</span><span class="p">,</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">ETableFieldType</span><span class="p">(</span><span class="n" style="color: #333;">ctfGFF_geneID</span><span class="p">));</span></span>
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<td class="diff-line-num new new_line" data-linenumber="302" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
302
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<pre style="margin: 0;">+<span id="LC302" class="line" lang="cpp"> <span class="n" style="color: #333;">specialFields</span><span class="p">.</span><span class="n" style="color: #333;">Add</span><span class="p">(</span><span class="s" style="color: #d14;">"genename"</span><span class="p">,</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">ETableFieldType</span><span class="p">(</span><span class="n" style="color: #333;">ctfGFF_geneName</span><span class="p">));</span></span>
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<td class="diff-line-num old_line" data-linenumber="299" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
299
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<td class="diff-line-num new_line" data-linenumber="303" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
303
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<pre style="margin: 0;"> <span id="LC303" class="line" lang="cpp"> <span class="n" style="color: #333;">specialFields</span><span class="p">.</span><span class="n" style="color: #333;">Add</span><span class="p">(</span><span class="s" style="color: #d14;">"parent"</span><span class="p">,</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">ETableFieldType</span><span class="p">(</span><span class="n" style="color: #333;">ctfGFF_Parent</span><span class="p">));</span></span>
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300
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<td class="diff-line-num new_line" data-linenumber="304" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
304
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<pre style="margin: 0;"> <span id="LC304" class="line" lang="cpp"> <span class="n" style="color: #333;">specialFields</span><span class="p">.</span><span class="n" style="color: #333;">Add</span><span class="p">(</span><span class="s" style="color: #d14;">"feature"</span><span class="p">,</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">ETableFieldType</span><span class="p">(</span><span class="n" style="color: #333;">ctfGFF_feature</span><span class="p">));</span></span>
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<td class="diff-line-num old_line" data-linenumber="301" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
301
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<td class="diff-line-num new_line" data-linenumber="305" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
305
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<pre style="margin: 0;"> <span id="LC305" class="line" lang="cpp"> <span class="n" style="color: #333;">specialFields</span><span class="p">.</span><span class="n" style="color: #333;">Add</span><span class="p">(</span><span class="s" style="color: #d14;">"start"</span><span class="p">,</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">ETableFieldType</span><span class="p">(</span><span class="n" style="color: #333;">ctfGFF_start</span><span class="p">));</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="312" style="width: 35px; color: rgba(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="316" style="width: 35px; color: rgba(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">@@ -312,6 +316,7 @@ void setTableFormat(GStr& s) {</td>
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<td class="diff-line-num old_line" data-linenumber="312" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
312
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<td class="diff-line-num new_line" data-linenumber="316" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
316
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<pre style="margin: 0;"> <span id="LC316" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">nextToken</span><span class="p">(</span><span class="n" style="color: #333;">w</span><span class="p">))</span> <span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="313" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
313
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<td class="diff-line-num new_line" data-linenumber="317" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
317
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<pre style="margin: 0;"> <span id="LC317" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">w</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span><span class="o" style="font-weight: 600;">==</span><span class="sc" style="color: #d14;">'@'</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="314" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
314
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<td class="diff-line-num new_line" data-linenumber="318" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
318
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<pre style="margin: 0;"> <span id="LC318" class="line" lang="cpp"> <span class="n" style="color: #333;">w</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">w</span><span class="p">.</span><span class="n" style="color: #333;">substr</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="319" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
319
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<pre style="margin: 0;">+<span id="LC319" class="line" lang="cpp"> <span class="n" style="color: #333;">w</span><span class="p">.</span><span class="n" style="color: #333;">lower</span><span class="p">();</span></span>
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<td class="diff-line-num old_line" data-linenumber="315" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
315
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320
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<pre style="margin: 0;"> <span id="LC320" class="line" lang="cpp"> <span class="n" style="color: #333;">ETableFieldType</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">v</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">specialFields</span><span class="p">.</span><span class="n" style="color: #333;">Find</span><span class="p">(</span><span class="n" style="color: #333;">w</span><span class="p">.</span><span class="n" style="color: #333;">chars</span><span class="p">());</span></span>
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316
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321
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<pre style="margin: 0;"> <span id="LC321" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">v</span><span class="o" style="font-weight: 600;">!=</span><span class="nb" style="color: #0086b3;">NULL</span><span class="p">)</span> <span class="p">{</span></span>
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317
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322
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<pre style="margin: 0;"> <span id="LC322" class="line" lang="cpp"> <span class="n" style="color: #333;">CTableField</span> <span class="n" style="color: #333;">tcol</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">v</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="330" style="width: 35px; color: rgba(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="335" style="width: 35px; color: rgba(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">@@ -330,6 +335,11 @@ void setTableFormat(GStr& s) {</td>
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330
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335
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<pre style="margin: 0;"> <span id="LC335" class="line" lang="cpp"> <span class="n" style="color: #333;">tableCols</span><span class="p">.</span><span class="n" style="color: #333;">Add</span><span class="p">(</span><span class="n" style="color: #333;">tcol</span><span class="p">);</span></span>
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331
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336
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<pre style="margin: 0;"> <span id="LC336" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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332
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337
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<pre style="margin: 0;"> <span id="LC337" class="line" lang="cpp"> <span class="p">}</span></span>
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338
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<pre style="margin: 0;">+<span id="LC338" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">w</span><span class="o" style="font-weight: 600;">==</span><span class="s" style="color: #d14;">"geneID"</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">w</span><span class="o" style="font-weight: 600;">==</span><span class="s" style="color: #d14;">"gene_id"</span><span class="p">)</span> <span class="p">{</span></span>
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339
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<pre style="margin: 0;">+<span id="LC339" class="line" lang="cpp"> <span class="n" style="color: #333;">CTableField</span> <span class="n" style="color: #333;">tcol</span><span class="p">(</span><span class="n" style="color: #333;">ctfGFF_geneID</span><span class="p">);</span></span>
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340
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<pre style="margin: 0;">+<span id="LC340" class="line" lang="cpp"> <span class="n" style="color: #333;">tableCols</span><span class="p">.</span><span class="n" style="color: #333;">Add</span><span class="p">(</span><span class="n" style="color: #333;">tcol</span><span class="p">);</span></span>
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341
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<pre style="margin: 0;">+<span id="LC341" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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342
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<pre style="margin: 0;">+<span id="LC342" class="line" lang="cpp"> <span class="p">}</span></span>
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333
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343
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<pre style="margin: 0;"> <span id="LC343" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">w</span><span class="o" style="font-weight: 600;">==</span><span class="s" style="color: #d14;">"Parent"</span><span class="p">)</span> <span class="p">{</span></span>
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334
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344
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<pre style="margin: 0;"> <span id="LC344" class="line" lang="cpp"> <span class="n" style="color: #333;">CTableField</span> <span class="n" style="color: #333;">tcol</span><span class="p">(</span><span class="n" style="color: #333;">ctfGFF_Parent</span><span class="p">);</span></span>
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335
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345
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<pre style="margin: 0;"> <span id="LC345" class="line" lang="cpp"> <span class="n" style="color: #333;">tableCols</span><span class="p">.</span><span class="n" style="color: #333;">Add</span><span class="p">(</span><span class="n" style="color: #333;">tcol</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="431" style="width: 35px; color: rgba(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="441" style="width: 35px; color: rgba(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">@@ -431,6 +441,88 @@ int adjust_stopcodon(GffObj& gffrec, int adj, GList<GSeg>* seglst=NULL) {</td>
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431
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441
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<pre style="margin: 0;"> <span id="LC441" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">realadj</span><span class="p">;</span></span>
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432
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442
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<pre style="margin: 0;"> <span id="LC442" class="line" lang="cpp"> <span class="p">}</span></span>
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433
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443
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<pre style="margin: 0;"> <span id="LC443" class="line" lang="cpp"></span>
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444
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<pre style="margin: 0;">+<span id="LC444" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">printTableData</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">FILE</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">f</span><span class="p">,</span> <span class="n" style="color: #333;">GffObj</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;">bool</span> <span class="n" style="color: #333;">inFasta</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">false</span><span class="p">)</span> <span class="p">{</span></span>
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445
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<pre style="margin: 0;">+<span id="LC445" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//using attribute list in tableCols</span></span>
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446
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<pre style="margin: 0;">+<span id="LC446" class="line" lang="cpp"> <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;">av</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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447
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<pre style="margin: 0;">+<span id="LC447" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</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;">tableCols</span><span class="p">.</span><span class="n" style="color: #333;">Count</span><span class="p">();</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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448
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<pre style="margin: 0;">+<span id="LC448" class="line" lang="cpp"> <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="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">inFasta</span><span class="p">)</span> <span class="p">{</span></span>
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449
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<pre style="margin: 0;">+<span id="LC449" class="line" lang="cpp"> <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;">inFasta</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">tableCols</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">type</span><span class="o" style="font-weight: 600;">!=</span><span class="n" style="color: #333;">ctfGFF_ID</span><span class="p">)</span></span>
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450
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<pre style="margin: 0;">+<span id="LC450" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">f</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;">"</span><span class="p">);</span></span>
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451
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<pre style="margin: 0;">+<span id="LC451" class="line" lang="cpp"> <span class="p">}</span></span>
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452
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<pre style="margin: 0;">+<span id="LC452" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">switch</span><span class="p">(</span><span class="n" style="color: #333;">tableCols</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">type</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="453" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
453
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<pre style="margin: 0;">+<span id="LC453" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">ctfGFF_Attr</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="454" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
454
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<pre style="margin: 0;">+<span id="LC454" class="line" lang="cpp"> <span class="n" style="color: #333;">av</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">g</span><span class="p">.</span><span class="n" style="color: #333;">getAttr</span><span class="p">(</span><span class="n" style="color: #333;">tableCols</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">name</span><span class="p">.</span><span class="n" style="color: #333;">chars</span><span class="p">());</span></span>
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455
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<pre style="margin: 0;">+<span id="LC455" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">,</span><span class="s" style="color: #d14;">"%s"</span><span class="p">,</span><span class="n" style="color: #333;">av</span><span class="o" style="font-weight: 600;">!=</span><span class="nb" style="color: #0086b3;">NULL</span><span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">av</span> <span class="o" style="font-weight: 600;">:</span> <span class="s" style="color: #d14;">"."</span><span class="p">);</span></span>
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456
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<pre style="margin: 0;">+<span id="LC456" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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457
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<pre style="margin: 0;">+<span id="LC457" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">ctfGFF_chr</span><span class="p">:</span></span>
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458
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<pre style="margin: 0;">+<span id="LC458" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">,</span><span class="s" style="color: #d14;">"%s"</span><span class="p">,</span><span class="n" style="color: #333;">g</span><span class="p">.</span><span class="n" style="color: #333;">getGSeqName</span><span class="p">());</span></span>
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459
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<pre style="margin: 0;">+<span id="LC459" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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460
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<pre style="margin: 0;">+<span id="LC460" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">ctfGFF_ID</span><span class="p">:</span></span>
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461
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<pre style="margin: 0;">+<span id="LC461" class="line" lang="cpp"> <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;">inFasta</span><span class="p">)</span></span>
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462
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<pre style="margin: 0;">+<span id="LC462" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">,</span><span class="s" style="color: #d14;">"%s"</span><span class="p">,</span><span class="n" style="color: #333;">g</span><span class="p">.</span><span class="n" style="color: #333;">getID</span><span class="p">());</span></span>
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463
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<pre style="margin: 0;">+<span id="LC463" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="464" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
464
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<pre style="margin: 0;">+<span id="LC464" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">ctfGFF_geneID</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="465" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
465
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<pre style="margin: 0;">+<span id="LC465" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">,</span><span class="s" style="color: #d14;">"%s"</span><span class="p">,</span><span class="n" style="color: #333;">g</span><span class="p">.</span><span class="n" style="color: #333;">getGeneID</span><span class="p">()</span><span class="o" style="font-weight: 600;">!=</span><span class="nb" style="color: #0086b3;">NULL</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">g</span><span class="p">.</span><span class="n" style="color: #333;">getGeneID</span><span class="p">()</span> <span class="o" style="font-weight: 600;">:</span> <span class="s" style="color: #d14;">"."</span><span class="p">);</span></span>
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466
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<pre style="margin: 0;">+<span id="LC466" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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467
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<pre style="margin: 0;">+<span id="LC467" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">ctfGFF_geneName</span><span class="p">:</span></span>
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468
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<pre style="margin: 0;">+<span id="LC468" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">,</span><span class="s" style="color: #d14;">"%s"</span><span class="p">,</span><span class="n" style="color: #333;">g</span><span class="p">.</span><span class="n" style="color: #333;">getGeneName</span><span class="p">()</span><span class="o" style="font-weight: 600;">!=</span><span class="nb" style="color: #0086b3;">NULL</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">g</span><span class="p">.</span><span class="n" style="color: #333;">getGeneName</span><span class="p">()</span> <span class="o" style="font-weight: 600;">:</span> <span class="s" style="color: #d14;">"."</span><span class="p">);</span></span>
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469
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<pre style="margin: 0;">+<span id="LC469" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="470" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
470
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<pre style="margin: 0;">+<span id="LC470" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">ctfGFF_Parent</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="471" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
471
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<pre style="margin: 0;">+<span id="LC471" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">,</span><span class="s" style="color: #d14;">"%s"</span><span class="p">,</span><span class="n" style="color: #333;">g</span><span class="p">.</span><span class="n" style="color: #333;">parent</span><span class="o" style="font-weight: 600;">!=</span><span class="nb" style="color: #0086b3;">NULL</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">g</span><span class="p">.</span><span class="n" style="color: #333;">parent</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getID</span><span class="p">()</span> <span class="o" style="font-weight: 600;">:</span> <span class="s" style="color: #d14;">"."</span><span class="p">);</span></span>
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472
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<pre style="margin: 0;">+<span id="LC472" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="473" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
473
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<pre style="margin: 0;">+<span id="LC473" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">ctfGFF_feature</span><span class="p">:</span></span>
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474
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<pre style="margin: 0;">+<span id="LC474" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">,</span><span class="s" style="color: #d14;">"%s"</span><span class="p">,</span><span class="n" style="color: #333;">g</span><span class="p">.</span><span class="n" style="color: #333;">getFeatureName</span><span class="p">());</span></span>
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475
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<pre style="margin: 0;">+<span id="LC475" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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476
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<pre style="margin: 0;">+<span id="LC476" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">ctfGFF_start</span><span class="p">:</span></span>
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477
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<pre style="margin: 0;">+<span id="LC477" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">,</span><span class="s" style="color: #d14;">"%d"</span><span class="p">,</span><span class="n" style="color: #333;">g</span><span class="p">.</span><span class="n" style="color: #333;">start</span><span class="p">);</span></span>
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478
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<pre style="margin: 0;">+<span id="LC478" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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479
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<pre style="margin: 0;">+<span id="LC479" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">ctfGFF_end</span><span class="p">:</span></span>
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480
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<pre style="margin: 0;">+<span id="LC480" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">,</span><span class="s" style="color: #d14;">"%d"</span><span class="p">,</span><span class="n" style="color: #333;">g</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="481" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
481
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<pre style="margin: 0;">+<span id="LC481" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="482" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
482
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<pre style="margin: 0;">+<span id="LC482" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">ctfGFF_strand</span><span class="p">:</span></span>
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483
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<pre style="margin: 0;">+<span id="LC483" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">,</span><span class="s" style="color: #d14;">"%c"</span><span class="p">,</span><span class="n" style="color: #333;">g</span><span class="p">.</span><span class="n" style="color: #333;">strand</span><span class="p">);</span></span>
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484
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<pre style="margin: 0;">+<span id="LC484" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="485" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
485
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<pre style="margin: 0;">+<span id="LC485" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">ctfGFF_numexons</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="486" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
486
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<pre style="margin: 0;">+<span id="LC486" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">,</span><span class="s" style="color: #d14;">"%d"</span><span class="p">,</span><span class="n" style="color: #333;">g</span><span class="p">.</span><span class="n" style="color: #333;">exons</span><span class="p">.</span><span class="n" style="color: #333;">Count</span><span class="p">());</span></span>
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<td class="diff-line-num new new_line" data-linenumber="487" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
487
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<pre style="margin: 0;">+<span id="LC487" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="488" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
488
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<pre style="margin: 0;">+<span id="LC488" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">ctfGFF_exons</span><span class="p">:</span></span>
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489
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<pre style="margin: 0;">+<span id="LC489" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">g</span><span class="p">.</span><span class="n" style="color: #333;">exons</span><span class="p">.</span><span class="n" style="color: #333;">Count</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="490" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
490
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<pre style="margin: 0;">+<span id="LC490" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">x</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;">x</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">g</span><span class="p">.</span><span class="n" style="color: #333;">exons</span><span class="p">.</span><span class="n" style="color: #333;">Count</span><span class="p">();</span><span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="491" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
491
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<pre style="margin: 0;">+<span id="LC491" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</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;">0</span><span class="p">)</span> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">,</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="492" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
492
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<pre style="margin: 0;">+<span id="LC492" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">,</span><span class="s" style="color: #d14;">"%d-%d"</span><span class="p">,</span><span class="n" style="color: #333;">g</span><span class="p">.</span><span class="n" style="color: #333;">exons</span><span class="p">[</span><span class="n" style="color: #333;">x</span><span class="p">]</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="n" style="color: #333;">g</span><span class="p">.</span><span class="n" style="color: #333;">exons</span><span class="p">[</span><span class="n" style="color: #333;">x</span><span class="p">]</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">end</span><span class="p">);</span></span>
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493
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<pre style="margin: 0;">+<span id="LC493" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="494" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
494
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<pre style="margin: 0;">+<span id="LC494" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">,</span><span class="s" style="color: #d14;">"."</span><span class="p">);</span></span>
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495
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<pre style="margin: 0;">+<span id="LC495" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="496" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
496
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<pre style="margin: 0;">+<span id="LC496" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">ctfGFF_cds</span><span class="p">:</span></span>
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497
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<pre style="margin: 0;">+<span id="LC497" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">g</span><span class="p">.</span><span class="n" style="color: #333;">hasCDS</span><span class="p">())</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="498" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
498
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<pre style="margin: 0;">+<span id="LC498" class="line" lang="cpp"> <span class="n" style="color: #333;">GVec</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">GffExon</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">cds</span><span class="p">;</span></span>
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499
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<pre style="margin: 0;">+<span id="LC499" class="line" lang="cpp"> <span class="n" style="color: #333;">g</span><span class="p">.</span><span class="n" style="color: #333;">getCDSegs</span><span class="p">(</span><span class="n" style="color: #333;">cds</span><span class="p">);</span></span>
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500
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<pre style="margin: 0;">+<span id="LC500" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">x</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;">x</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">cds</span><span class="p">.</span><span class="n" style="color: #333;">Count</span><span class="p">();</span><span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="501" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
501
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<pre style="margin: 0;">+<span id="LC501" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</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;">0</span><span class="p">)</span> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">,</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="502" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
502
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<pre style="margin: 0;">+<span id="LC502" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">,</span><span class="s" style="color: #d14;">"%d-%d"</span><span class="p">,</span><span class="n" style="color: #333;">cds</span><span class="p">[</span><span class="n" style="color: #333;">x</span><span class="p">].</span><span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="n" style="color: #333;">cds</span><span class="p">[</span><span class="n" style="color: #333;">x</span><span class="p">].</span><span class="n" style="color: #333;">end</span><span class="p">);</span></span>
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503
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<pre style="margin: 0;">+<span id="LC503" class="line" lang="cpp"> <span class="p">}</span></span>
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504
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<pre style="margin: 0;">+<span id="LC504" class="line" lang="cpp"> <span class="p">}</span></span>
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505
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<pre style="margin: 0;">+<span id="LC505" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">,</span><span class="s" style="color: #d14;">"."</span><span class="p">);</span></span>
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506
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<pre style="margin: 0;">+<span id="LC506" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="507" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
507
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<pre style="margin: 0;">+<span id="LC507" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">ctfGFF_covlen</span><span class="p">:</span></span>
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508
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<pre style="margin: 0;">+<span id="LC508" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">,</span> <span class="s" style="color: #d14;">"%d"</span><span class="p">,</span> <span class="n" style="color: #333;">g</span><span class="p">.</span><span class="n" style="color: #333;">covlen</span><span class="p">);</span></span>
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509
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<pre style="margin: 0;">+<span id="LC509" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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510
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<pre style="margin: 0;">+<span id="LC510" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">ctfGFF_cdslen</span><span class="p">:</span></span>
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511
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<pre style="margin: 0;">+<span id="LC511" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">g</span><span class="p">.</span><span class="n" style="color: #333;">hasCDS</span><span class="p">())</span> <span class="p">{</span></span>
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512
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<pre style="margin: 0;">+<span id="LC512" class="line" lang="cpp"> <span class="n" style="color: #333;">GVec</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">GffExon</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">cds</span><span class="p">;</span></span>
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513
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<pre style="margin: 0;">+<span id="LC513" class="line" lang="cpp"> <span class="n" style="color: #333;">g</span><span class="p">.</span><span class="n" style="color: #333;">getCDSegs</span><span class="p">(</span><span class="n" style="color: #333;">cds</span><span class="p">);</span></span>
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514
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<pre style="margin: 0;">+<span id="LC514" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">clen</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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515
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<pre style="margin: 0;">+<span id="LC515" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">x</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;">x</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">cds</span><span class="p">.</span><span class="n" style="color: #333;">Count</span><span class="p">();</span><span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>
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516
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<pre style="margin: 0;">+<span id="LC516" class="line" lang="cpp"> <span class="n" style="color: #333;">clen</span><span class="o" style="font-weight: 600;">+=</span><span class="n" style="color: #333;">cds</span><span class="p">[</span><span class="n" style="color: #333;">x</span><span class="p">].</span><span class="n" style="color: #333;">end</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">cds</span><span class="p">[</span><span class="n" style="color: #333;">x</span><span class="p">].</span><span class="n" style="color: #333;">start</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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517
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<pre style="margin: 0;">+<span id="LC517" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">,</span> <span class="s" style="color: #d14;">"%d"</span><span class="p">,</span> <span class="n" style="color: #333;">clen</span><span class="p">);</span></span>
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518
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<pre style="margin: 0;">+<span id="LC518" class="line" lang="cpp"> <span class="p">}</span></span>
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519
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<pre style="margin: 0;">+<span id="LC519" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">,</span> <span class="s" style="color: #d14;">"0"</span><span class="p">);</span></span>
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520
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<pre style="margin: 0;">+<span id="LC520" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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521
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<pre style="margin: 0;">+<span id="LC521" class="line" lang="cpp"> <span class="p">}</span> <span class="c1" style="color: #998; font-style: italic;">//switch</span></span>
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522
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<pre style="margin: 0;">+<span id="LC522" class="line" lang="cpp"> <span class="p">}</span></span>
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523
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<pre style="margin: 0;">+<span id="LC523" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">,</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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524
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<pre style="margin: 0;">+<span id="LC524" class="line" lang="cpp"><span class="p">}</span></span>
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525
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<pre style="margin: 0;">+<span id="LC525" class="line" lang="cpp"></span>
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526
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<pre style="margin: 0;"> <span id="LC526" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="nf" style="color: #900; font-weight: 600;">process_transcript</span><span class="p">(</span><span class="n" style="color: #333;">GFastaDb</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">gfasta</span><span class="p">,</span> <span class="n" style="color: #333;">GffObj</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">gffrec</span><span class="p">)</span> <span class="p">{</span></span>
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435
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527
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<pre style="margin: 0;"> <span id="LC527" class="line" lang="cpp"> <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;">gffrec</span><span class="p">.</span><span class="n" style="color: #333;">isTranscript</span><span class="p">())</span> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">//shouldn't call this function unless it's a transcript</span></span>
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436
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528
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<pre style="margin: 0;"> <span id="LC528" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//returns true if the transcript passed the filter</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">@@ -650,25 +742,16 @@ bool process_transcript(GFastaDb& gfasta, GffObj& gffrec) {</td>
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<pre style="margin: 0;"> <span id="LC742" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">cdsaa</span><span class="o" style="font-weight: 600;">==</span><span class="nb" style="color: #0086b3;">NULL</span><span class="p">)</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">//translate now if not done before</span></span>
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<pre style="margin: 0;"> <span id="LC743" class="line" lang="cpp"> <span class="n" style="color: #333;">cdsaa</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">translateDNA</span><span class="p">(</span><span class="n" style="color: #333;">cdsnt</span><span class="p">,</span> <span class="n" style="color: #333;">aalen</span><span class="p">,</span> <span class="n" style="color: #333;">seqlen</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC744" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC653" class="line" lang="cpp"> <span class="n" style="color: #333;">GStr</span> <span class="n" style="color: #333;">defline</span><span class="p">(</span><span class="n" style="color: #333;">gffrec</span><span class="p">.</span><span class="n" style="color: #333;">getID</span><span class="p">());</span></span>
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<pre style="margin: 0;">-<span id="LC654" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">gffrec</span><span class="p">.</span><span class="n" style="color: #333;">attrs</span><span class="o" style="font-weight: 600;">!=</span><span class="nb" style="color: #0086b3;">NULL</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC655" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//append all attributes found for each transcripts</span></span>
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<pre style="margin: 0;">-<span id="LC656" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</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;">gffrec</span><span class="p">.</span><span class="n" style="color: #333;">attrs</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Count</span><span class="p">();</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC657" class="line" lang="cpp"> <span class="n" style="color: #333;">defline</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="s" style="color: #d14;">" "</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC658" class="line" lang="cpp"> <span class="n" style="color: #333;">defline</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">gffrec</span><span class="p">.</span><span class="n" style="color: #333;">getAttrName</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">));</span></span>
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<pre style="margin: 0;">-<span id="LC659" class="line" lang="cpp"> <span class="n" style="color: #333;">defline</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="s" style="color: #d14;">"="</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC660" class="line" lang="cpp"> <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;">s</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">gffrec</span><span class="p">.</span><span class="n" style="color: #333;">getAttrValue</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC661" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span><span class="o" style="font-weight: 600;">==</span><span class="sc" style="color: #d14;">'"'</span><span class="p">)</span> <span class="n" style="color: #333;">defline</span><span class="p">.</span><span class="n" style="color: #333;">append</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="LC662" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">defline</span><span class="p">.</span><span class="n" style="color: #333;">appendQuoted</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">,</span> <span class="sc" style="color: #d14;">'{'</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC663" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC664" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC745" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">aalen</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="LC746" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">cdsaa</span><span class="p">[</span><span class="n" style="color: #333;">aalen</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">==</span><span class="sc" style="color: #d14;">'.'</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">cdsaa</span><span class="p">[</span><span class="n" style="color: #333;">aalen</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">==</span><span class="sc" style="color: #d14;">'\0'</span><span class="p">)</span> <span class="o" style="font-weight: 600;">--</span><span class="n" style="color: #333;">aalen</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">//avoid printing the stop codon</span></span>
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<pre style="margin: 0;">-<span id="LC667" class="line" lang="cpp"> <span class="n" style="color: #333;">printFasta</span><span class="p">(</span><span class="n" style="color: #333;">f_y</span><span class="p">,</span> <span class="n" style="color: #333;">defline</span><span class="p">,</span> <span class="n" style="color: #333;">cdsaa</span><span class="p">,</span> <span class="n" style="color: #333;">aalen</span><span class="p">,</span> <span class="n" style="color: #333;">StarStop</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC747" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">f_y</span><span class="p">,</span> <span class="s" style="color: #d14;">">%s"</span><span class="p">,</span> <span class="n" style="color: #333;">gffrec</span><span class="p">.</span><span class="n" style="color: #333;">getID</span><span class="p">());</span></span>
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748
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<pre style="margin: 0;">+<span id="LC748" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">fmtTable</span><span class="p">)</span> <span class="n" style="color: #333;">printTableData</span><span class="p">(</span><span class="n" style="color: #333;">f_y</span><span class="p">,</span> <span class="n" style="color: #333;">gffrec</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">);</span></span>
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749
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<pre style="margin: 0;">+<span id="LC749" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">f_y</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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750
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<pre style="margin: 0;">+<span id="LC750" class="line" lang="cpp"> <span class="n" style="color: #333;">printFasta</span><span class="p">(</span><span class="n" style="color: #333;">f_y</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="n" style="color: #333;">cdsaa</span><span class="p">,</span> <span class="n" style="color: #333;">aalen</span><span class="p">,</span> <span class="n" style="color: #333;">StarStop</span><span class="p">);</span></span>
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668
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751
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<pre style="margin: 0;"> <span id="LC751" class="line" lang="cpp"> <span class="p">}</span></span>
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669
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752
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<pre style="margin: 0;"> <span id="LC752" class="line" lang="cpp"> <span class="p">}</span></span>
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670
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753
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<pre style="margin: 0;"> <span id="LC753" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">f_x</span><span class="o" style="font-weight: 600;">!=</span><span class="nb" style="color: #0086b3;">NULL</span><span class="p">)</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">//CDS only</span></span>
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671
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<pre style="margin: 0;">-<span id="LC671" class="line" lang="cpp"> <span class="n" style="color: #333;">GStr</span> <span class="n" style="color: #333;">defline</span><span class="p">(</span><span class="n" style="color: #333;">gffrec</span><span class="p">.</span><span class="n" style="color: #333;">getID</span><span class="p">());</span></span>
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754
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<pre style="margin: 0;">+<span id="LC754" class="line" lang="cpp"> <span class="n" style="color: #333;">GStr</span> <span class="n" style="color: #333;">defline</span><span class="p">(</span><span class="n" style="color: #333;">gffrec</span><span class="p">.</span><span class="n" style="color: #333;">getID</span><span class="p">()<span class="idiff left">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">94</span></span><span class="p">);</span></span>
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672
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755
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<pre style="margin: 0;"> <span id="LC755" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">writeExonSegs</span><span class="p">)</span> <span class="p">{</span></span>
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673
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756
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<pre style="margin: 0;"> <span id="LC756" class="line" lang="cpp"> <span class="n" style="color: #333;">defline</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="s" style="color: #d14;">" loc:"</span><span class="p">);</span></span>
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674
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757
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<pre style="margin: 0;"> <span id="LC757" class="line" lang="cpp"> <span class="n" style="color: #333;">defline</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">gffrec</span><span class="p">.</span><span class="n" style="color: #333;">getGSeqName</span><span class="p">());</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="685" style="width: 35px; color: rgba(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="768" style="width: 35px; color: rgba(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">@@ -685,19 +768,11 @@ bool process_transcript(GFastaDb& gfasta, GffObj& gffrec) {</td>
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685
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768
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<pre style="margin: 0;"> <span id="LC768" class="line" lang="cpp"> <span class="n" style="color: #333;">defline</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="s" style="color: #d14;">"-"</span><span class="p">);</span></span>
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686
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769
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<pre style="margin: 0;"> <span id="LC769" class="line" lang="cpp"> <span class="n" style="color: #333;">defline</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;">seglst</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">end</span><span class="p">;</span></span>
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687
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770
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<pre style="margin: 0;"> <span id="LC770" class="line" lang="cpp"> <span class="p">}</span></span>
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688
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<pre style="margin: 0;">-<span id="LC688" class="line" lang="cpp"> <span class="p">}</span></span>
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689
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<pre style="margin: 0;">-<span id="LC689" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">gffrec</span><span class="p">.</span><span class="n" style="color: #333;">attrs</span><span class="o" style="font-weight: 600;">!=</span><span class="nb" style="color: #0086b3;">NULL</span><span class="p">)</span> <span class="p">{</span></span>
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690
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<pre style="margin: 0;">-<span id="LC690" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//append all attributes found for each transcript</span></span>
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691
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<pre style="margin: 0;">-<span id="LC691" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</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;">gffrec</span><span class="p">.</span><span class="n" style="color: #333;">attrs</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Count</span><span class="p">();</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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692
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<pre style="margin: 0;">-<span id="LC692" class="line" lang="cpp"> <span class="n" style="color: #333;">defline</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="s" style="color: #d14;">" "</span><span class="p">);</span></span>
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693
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<pre style="margin: 0;">-<span id="LC693" class="line" lang="cpp"> <span class="n" style="color: #333;">defline</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">gffrec</span><span class="p">.</span><span class="n" style="color: #333;">getAttrName</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">));</span></span>
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694
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<pre style="margin: 0;">-<span id="LC694" class="line" lang="cpp"> <span class="n" style="color: #333;">defline</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="s" style="color: #d14;">"="</span><span class="p">);</span></span>
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695
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<pre style="margin: 0;">-<span id="LC695" class="line" lang="cpp"> <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;">s</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">gffrec</span><span class="p">.</span><span class="n" style="color: #333;">getAttrValue</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">);</span></span>
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696
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<pre style="margin: 0;">-<span id="LC696" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span><span class="o" style="font-weight: 600;">==</span><span class="sc" style="color: #d14;">'"'</span><span class="p">)</span> <span class="n" style="color: #333;">defline</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">);</span></span>
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697
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<pre style="margin: 0;">-<span id="LC697" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">defline</span><span class="p">.</span><span class="n" style="color: #333;">appendQuoted</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">,</span> <span class="sc" style="color: #d14;">'{'</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">);</span></span>
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698
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<pre style="margin: 0;">-<span id="LC698" class="line" lang="cpp"> <span class="p">}</span></span>
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699
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<pre style="margin: 0;">-<span id="LC699" class="line" lang="cpp"> <span class="p">}</span></span>
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700
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<pre style="margin: 0;">-<span id="LC700" class="line" lang="cpp"> <span class="n" style="color: #333;">printFasta</span><span class="p">(</span><span class="n" style="color: #333;">f_x</span><span class="p">,</span> <span class="n" style="color: #333;">defline</span><span class="p">,</span> <span class="n" style="color: #333;">cdsnt</span><span class="p">,</span> <span class="n" style="color: #333;">seqlen</span><span class="p">);</span></span>
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771
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<pre style="margin: 0;">+<span id="LC771" class="line" lang="cpp"> <span class="p">}</span></span>
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772
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<pre style="margin: 0;">+<span id="LC772" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">f_x</span><span class="p">,</span> <span class="s" style="color: #d14;">">%s"</span><span class="p">,</span> <span class="n" style="color: #333;">defline</span><span class="p">.</span><span class="n" style="color: #333;">chars</span><span class="p">());</span></span>
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773
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<pre style="margin: 0;">+<span id="LC773" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">fmtTable</span><span class="p">)</span> <span class="n" style="color: #333;">printTableData</span><span class="p">(</span><span class="n" style="color: #333;">f_x</span><span class="p">,</span> <span class="n" style="color: #333;">gffrec</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">);</span></span>
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774
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<pre style="margin: 0;">+<span id="LC774" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">f_x</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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775
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<pre style="margin: 0;">+<span id="LC775" class="line" lang="cpp"> <span class="n" style="color: #333;">printFasta</span><span class="p">(</span><span class="n" style="color: #333;">f_x</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="n" style="color: #333;">cdsnt</span><span class="p">,</span> <span class="n" style="color: #333;">seqlen</span><span class="p">);</span></span>
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701
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776
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<pre style="margin: 0;"> <span id="LC776" class="line" lang="cpp"> <span class="p">}</span></span>
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702
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777
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<pre style="margin: 0;"> <span id="LC777" class="line" lang="cpp"> <span class="n" style="color: #333;">GFREE</span><span class="p">(</span><span class="n" style="color: #333;">cdsnt</span><span class="p">);</span></span>
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703
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778
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<pre style="margin: 0;"> <span id="LC778" class="line" lang="cpp"> <span class="n" style="color: #333;">GFREE</span><span class="p">(</span><span class="n" style="color: #333;">cdsaa</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="758" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="833" style="width: 35px; color: rgba(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">@@ -758,18 +833,10 @@ bool process_transcript(GFastaDb& gfasta, GffObj& gffrec) {</td>
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758
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833
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<pre style="margin: 0;"> <span id="LC833" class="line" lang="cpp"> <span class="p">}</span></span>
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759
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834
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<pre style="margin: 0;"> <span id="LC834" class="line" lang="cpp"> <span class="p">}</span></span>
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760
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835
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<pre style="margin: 0;"> <span id="LC835" class="line" lang="cpp"></span>
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761
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<pre style="margin: 0;">-<span id="LC761" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">gffrec</span><span class="p">.</span><span class="n" style="color: #333;">attrs</span><span class="o" style="font-weight: 600;">!=</span><span class="nb" style="color: #0086b3;">NULL</span><span class="p">)</span> <span class="p">{</span></span>
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762
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<pre style="margin: 0;">-<span id="LC762" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//append all attributes found for each transcripts</span></span>
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<pre style="margin: 0;">-<span id="LC763" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</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;">gffrec</span><span class="p">.</span><span class="n" style="color: #333;">attrs</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Count</span><span class="p">();</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC764" class="line" lang="cpp"> <span class="n" style="color: #333;">defline</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="s" style="color: #d14;">" "</span><span class="p">);</span></span>
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765
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<pre style="margin: 0;">-<span id="LC765" class="line" lang="cpp"> <span class="n" style="color: #333;">defline</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">gffrec</span><span class="p">.</span><span class="n" style="color: #333;">getAttrName</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">));</span></span>
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766
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<pre style="margin: 0;">-<span id="LC766" class="line" lang="cpp"> <span class="n" style="color: #333;">defline</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="s" style="color: #d14;">"="</span><span class="p">);</span></span>
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767
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<pre style="margin: 0;">-<span id="LC767" class="line" lang="cpp"> <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;">s</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">gffrec</span><span class="p">.</span><span class="n" style="color: #333;">getAttrValue</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">);</span></span>
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768
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<pre style="margin: 0;">-<span id="LC768" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span><span class="o" style="font-weight: 600;">==</span><span class="sc" style="color: #d14;">'"'</span><span class="p">)</span> <span class="n" style="color: #333;">defline</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">);</span></span>
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769
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<pre style="margin: 0;">-<span id="LC769" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">defline</span><span class="p">.</span><span class="n" style="color: #333;">appendQuoted</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">,</span> <span class="sc" style="color: #d14;">'{'</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">);</span></span>
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770
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<pre style="margin: 0;">-<span id="LC770" class="line" lang="cpp"> <span class="p">}</span></span>
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771
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<pre style="margin: 0;">-<span id="LC771" class="line" lang="cpp"> <span class="p">}</span></span>
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772
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<pre style="margin: 0;">-<span id="LC772" class="line" lang="cpp"> <span class="n" style="color: #333;">printFasta</span><span class="p">(</span><span class="n" style="color: #333;">f_w</span><span class="p">,</span> <span class="n" style="color: #333;">defline</span><span class="p">,</span> <span class="n" style="color: #333;">exont</span><span class="p">,</span> <span class="n" style="color: #333;">seqlen</span><span class="p">);</span></span>
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836
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<pre style="margin: 0;">+<span id="LC836" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">f_w</span><span class="p">,</span> <span class="s" style="color: #d14;">">%s"</span><span class="p">,</span> <span class="n" style="color: #333;">defline</span><span class="p">.</span><span class="n" style="color: #333;">chars</span><span class="p">());</span></span>
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837
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<pre style="margin: 0;">+<span id="LC837" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">fmtTable</span><span class="p">)</span> <span class="n" style="color: #333;">printTableData</span><span class="p">(</span><span class="n" style="color: #333;">f_w</span><span class="p">,</span> <span class="n" style="color: #333;">gffrec</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">);</span></span>
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838
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<pre style="margin: 0;">+<span id="LC838" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">f_w</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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839
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<pre style="margin: 0;">+<span id="LC839" class="line" lang="cpp"> <span class="n" style="color: #333;">printFasta</span><span class="p">(</span><span class="n" style="color: #333;">f_w</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="n" style="color: #333;">exont</span><span class="p">,</span> <span class="n" style="color: #333;">seqlen</span><span class="p">);</span></span>
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773
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840
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<pre style="margin: 0;"> <span id="LC840" class="line" lang="cpp"> <span class="n" style="color: #333;">GFREE</span><span class="p">(</span><span class="n" style="color: #333;">exont</span><span class="p">);</span></span>
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774
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841
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<pre style="margin: 0;"> <span id="LC841" class="line" lang="cpp"> <span class="p">}</span></span>
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775
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842
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<pre style="margin: 0;"> <span id="LC842" class="line" lang="cpp"> <span class="p">}</span> <span class="c1" style="color: #998; font-style: italic;">//writing f_w (spliced exons)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="941" style="width: 35px; color: rgba(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="1008" style="width: 35px; color: rgba(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">@@ -941,84 +1008,6 @@ void printGffObj(FILE* f, GffObj* gfo, GStr& locname, GffPrintMode exonPrinting,</td>
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941
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1008
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<pre style="margin: 0;"> <span id="LC1008" class="line" lang="cpp"> <span class="n" style="color: #333;">t</span><span class="p">.</span><span class="n" style="color: #333;">printGxf</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">,</span> <span class="n" style="color: #333;">exonPrinting</span><span class="p">,</span> <span class="n" style="color: #333;">tracklabel</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="n" style="color: #333;">decodeChars</span><span class="p">);</span></span>
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942
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1009
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<pre style="margin: 0;"> <span id="LC1009" class="line" lang="cpp"><span class="p">}</span></span>
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943
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1010
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<pre style="margin: 0;"> <span id="LC1010" class="line" lang="cpp"></span>
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944
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<pre style="margin: 0;">-<span id="LC944" class="line" lang="cpp"></span>
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945
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<pre style="margin: 0;">-<span id="LC945" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">printGxfTab</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">FILE</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">f</span><span class="p">,</span> <span class="n" style="color: #333;">GffObj</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">g</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="946" 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">
946
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<pre style="margin: 0;">-<span id="LC946" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//using attribute list in tableCols</span></span>
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947
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<pre style="margin: 0;">-<span id="LC947" class="line" lang="cpp"> <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;">av</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="948" 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">
948
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<pre style="margin: 0;">-<span id="LC948" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</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;">tableCols</span><span class="p">.</span><span class="n" style="color: #333;">Count</span><span class="p">();</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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949
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<pre style="margin: 0;">-<span id="LC949" class="line" lang="cpp"> <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="mi" style="color: #099;">0</span><span class="p">)</span> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">f</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;">"</span><span class="p">);</span></span>
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950
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<pre style="margin: 0;">-<span id="LC950" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">switch</span><span class="p">(</span><span class="n" style="color: #333;">tableCols</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">type</span><span class="p">)</span> <span class="p">{</span></span>
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951
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<pre style="margin: 0;">-<span id="LC951" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">ctfGFF_Attr</span><span class="p">:</span></span>
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952
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<pre style="margin: 0;">-<span id="LC952" class="line" lang="cpp"> <span class="n" style="color: #333;">av</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">g</span><span class="p">.</span><span class="n" style="color: #333;">getAttr</span><span class="p">(</span><span class="n" style="color: #333;">tableCols</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">name</span><span class="p">.</span><span class="n" style="color: #333;">chars</span><span class="p">());</span></span>
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953
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<pre style="margin: 0;">-<span id="LC953" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">av</span><span class="o" style="font-weight: 600;">!=</span><span class="nb" style="color: #0086b3;">NULL</span><span class="p">)</span> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">,</span><span class="s" style="color: #d14;">"%s"</span><span class="p">,</span><span class="n" style="color: #333;">av</span><span class="p">);</span></span>
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954
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<pre style="margin: 0;">-<span id="LC954" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">,</span> <span class="s" style="color: #d14;">"."</span><span class="p">);</span></span>
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955
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<pre style="margin: 0;">-<span id="LC955" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="956" 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">
956
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<pre style="margin: 0;">-<span id="LC956" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">ctfGFF_chr</span><span class="p">:</span></span>
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<td class="diff-line-num old old_line" data-linenumber="957" 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">
957
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<pre style="margin: 0;">-<span id="LC957" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">,</span><span class="s" style="color: #d14;">"%s"</span><span class="p">,</span><span class="n" style="color: #333;">g</span><span class="p">.</span><span class="n" style="color: #333;">getGSeqName</span><span class="p">());</span></span>
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<td class="diff-line-num old old_line" data-linenumber="958" 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">
958
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<td class="diff-line-num new_line old" data-linenumber="1011" 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="LC958" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="959" 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">
959
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<td class="diff-line-num new_line old" data-linenumber="1011" 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="LC959" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">ctfGFF_ID</span><span class="p">:</span></span>
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<td class="diff-line-num old old_line" data-linenumber="960" 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">
960
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<td class="diff-line-num new_line old" data-linenumber="1011" 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="LC960" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">,</span><span class="s" style="color: #d14;">"%s"</span><span class="p">,</span><span class="n" style="color: #333;">g</span><span class="p">.</span><span class="n" style="color: #333;">getID</span><span class="p">());</span></span>
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<td class="diff-line-num old old_line" data-linenumber="961" 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">
961
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<pre style="margin: 0;">-<span id="LC961" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="962" 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">
962
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<td class="diff-line-num new_line old" data-linenumber="1011" 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="LC962" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">ctfGFF_geneID</span><span class="p">:</span></span>
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<td class="diff-line-num old old_line" data-linenumber="963" 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">
963
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<pre style="margin: 0;">-<span id="LC963" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">,</span><span class="s" style="color: #d14;">"%s"</span><span class="p">,</span><span class="n" style="color: #333;">g</span><span class="p">.</span><span class="n" style="color: #333;">getGeneID</span><span class="p">());</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="964" 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">
964
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<td class="diff-line-num new_line old" data-linenumber="1011" 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="LC964" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="965" 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">
965
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<td class="diff-line-num new_line old" data-linenumber="1011" 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="LC965" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">ctfGFF_Parent</span><span class="p">:</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="966" 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">
966
</td>
<td class="diff-line-num new_line old" data-linenumber="1011" 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="LC966" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">g</span><span class="p">.</span><span class="n" style="color: #333;">parent</span><span class="o" style="font-weight: 600;">!=</span><span class="nb" style="color: #0086b3;">NULL</span><span class="p">)</span> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">,</span><span class="s" style="color: #d14;">"%s"</span><span class="p">,</span><span class="n" style="color: #333;">g</span><span class="p">.</span><span class="n" style="color: #333;">parent</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getID</span><span class="p">());</span></span>
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<td class="diff-line-num old old_line" data-linenumber="967" 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">
967
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<td class="diff-line-num new_line old" data-linenumber="1011" 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="LC967" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">,</span> <span class="s" style="color: #d14;">"."</span><span class="p">);</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="968" 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">
968
</td>
<td class="diff-line-num new_line old" data-linenumber="1011" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC968" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="969" 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">
969
</td>
<td class="diff-line-num new_line old" data-linenumber="1011" 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="LC969" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">ctfGFF_feature</span><span class="p">:</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="970" 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">
970
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<td class="diff-line-num new_line old" data-linenumber="1011" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC970" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">,</span><span class="s" style="color: #d14;">"%s"</span><span class="p">,</span><span class="n" style="color: #333;">g</span><span class="p">.</span><span class="n" style="color: #333;">getFeatureName</span><span class="p">());</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="971" 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">
971
</td>
<td class="diff-line-num new_line old" data-linenumber="1011" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC971" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="972" 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">
972
</td>
<td class="diff-line-num new_line old" data-linenumber="1011" 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="LC972" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">ctfGFF_start</span><span class="p">:</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="973" 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">
973
</td>
<td class="diff-line-num new_line old" data-linenumber="1011" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC973" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">,</span><span class="s" style="color: #d14;">"%d"</span><span class="p">,</span><span class="n" style="color: #333;">g</span><span class="p">.</span><span class="n" style="color: #333;">start</span><span class="p">);</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="974" 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">
974
</td>
<td class="diff-line-num new_line old" data-linenumber="1011" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC974" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
</pre>
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<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="975" 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">
975
</td>
<td class="diff-line-num new_line old" data-linenumber="1011" 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="LC975" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">ctfGFF_end</span><span class="p">:</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="976" 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">
976
</td>
<td class="diff-line-num new_line old" data-linenumber="1011" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC976" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">,</span><span class="s" style="color: #d14;">"%d"</span><span class="p">,</span><span class="n" style="color: #333;">g</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">);</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="977" 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">
977
</td>
<td class="diff-line-num new_line old" data-linenumber="1011" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC977" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="978" 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">
978
</td>
<td class="diff-line-num new_line old" data-linenumber="1011" 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="LC978" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">ctfGFF_strand</span><span class="p">:</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="979" 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">
979
</td>
<td class="diff-line-num new_line old" data-linenumber="1011" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC979" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">,</span><span class="s" style="color: #d14;">"%c"</span><span class="p">,</span><span class="n" style="color: #333;">g</span><span class="p">.</span><span class="n" style="color: #333;">strand</span><span class="p">);</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="980" 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">
980
</td>
<td class="diff-line-num new_line old" data-linenumber="1011" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC980" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
</pre>
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<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="981" 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">
981
</td>
<td class="diff-line-num new_line old" data-linenumber="1011" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC981" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">ctfGFF_numexons</span><span class="p">:</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="982" 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">
982
</td>
<td class="diff-line-num new_line old" data-linenumber="1011" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC982" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">,</span><span class="s" style="color: #d14;">"%d"</span><span class="p">,</span><span class="n" style="color: #333;">g</span><span class="p">.</span><span class="n" style="color: #333;">exons</span><span class="p">.</span><span class="n" style="color: #333;">Count</span><span class="p">());</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="983" 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">
983
</td>
<td class="diff-line-num new_line old" data-linenumber="1011" 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">
</td>
<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC983" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
</pre>
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<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="984" 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">
984
</td>
<td class="diff-line-num new_line old" data-linenumber="1011" 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="LC984" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">ctfGFF_exons</span><span class="p">:</span></span>
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985
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<pre style="margin: 0;">-<span id="LC985" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">g</span><span class="p">.</span><span class="n" style="color: #333;">exons</span><span class="p">.</span><span class="n" style="color: #333;">Count</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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986
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<pre style="margin: 0;">-<span id="LC986" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">x</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;">x</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">g</span><span class="p">.</span><span class="n" style="color: #333;">exons</span><span class="p">.</span><span class="n" style="color: #333;">Count</span><span class="p">();</span><span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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987
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<pre style="margin: 0;">-<span id="LC987" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</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;">0</span><span class="p">)</span> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">,</span><span class="s" style="color: #d14;">","</span><span class="p">);</span></span>
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988
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<pre style="margin: 0;">-<span id="LC988" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">,</span><span class="s" style="color: #d14;">"%d-%d"</span><span class="p">,</span><span class="n" style="color: #333;">g</span><span class="p">.</span><span class="n" style="color: #333;">exons</span><span class="p">[</span><span class="n" style="color: #333;">x</span><span class="p">]</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="n" style="color: #333;">g</span><span class="p">.</span><span class="n" style="color: #333;">exons</span><span class="p">[</span><span class="n" style="color: #333;">x</span><span class="p">]</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">end</span><span class="p">);</span></span>
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989
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<pre style="margin: 0;">-<span id="LC989" class="line" lang="cpp"> <span class="p">}</span></span>
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990
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<pre style="margin: 0;">-<span id="LC990" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">,</span><span class="s" style="color: #d14;">"."</span><span class="p">);</span></span>
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991
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<pre style="margin: 0;">-<span id="LC991" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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992
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<pre style="margin: 0;">-<span id="LC992" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">ctfGFF_cds</span><span class="p">:</span></span>
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993
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<pre style="margin: 0;">-<span id="LC993" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">g</span><span class="p">.</span><span class="n" style="color: #333;">hasCDS</span><span class="p">())</span> <span class="p">{</span></span>
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994
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<pre style="margin: 0;">-<span id="LC994" class="line" lang="cpp"> <span class="n" style="color: #333;">GVec</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">GffExon</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">cds</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="995" 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">
995
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<pre style="margin: 0;">-<span id="LC995" class="line" lang="cpp"> <span class="n" style="color: #333;">g</span><span class="p">.</span><span class="n" style="color: #333;">getCDSegs</span><span class="p">(</span><span class="n" style="color: #333;">cds</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="996" 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">
996
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<pre style="margin: 0;">-<span id="LC996" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">x</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;">x</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">cds</span><span class="p">.</span><span class="n" style="color: #333;">Count</span><span class="p">();</span><span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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997
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<pre style="margin: 0;">-<span id="LC997" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</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;">0</span><span class="p">)</span> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">,</span><span class="s" style="color: #d14;">","</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="998" 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">
998
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<pre style="margin: 0;">-<span id="LC998" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">,</span><span class="s" style="color: #d14;">"%d-%d"</span><span class="p">,</span><span class="n" style="color: #333;">cds</span><span class="p">[</span><span class="n" style="color: #333;">x</span><span class="p">].</span><span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="n" style="color: #333;">cds</span><span class="p">[</span><span class="n" style="color: #333;">x</span><span class="p">].</span><span class="n" style="color: #333;">end</span><span class="p">);</span></span>
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999
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<pre style="margin: 0;">-<span id="LC999" class="line" lang="cpp"> <span class="p">}</span></span>
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1000
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<pre style="margin: 0;">-<span id="LC1000" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1001" 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">
1001
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<pre style="margin: 0;">-<span id="LC1001" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">,</span><span class="s" style="color: #d14;">"."</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1002" 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">
1002
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<pre style="margin: 0;">-<span id="LC1002" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1003" 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">
1003
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<pre style="margin: 0;">-<span id="LC1003" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">ctfGFF_covlen</span><span class="p">:</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1004" 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">
1004
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<pre style="margin: 0;">-<span id="LC1004" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">,</span> <span class="s" style="color: #d14;">"%d"</span><span class="p">,</span> <span class="n" style="color: #333;">g</span><span class="p">.</span><span class="n" style="color: #333;">covlen</span><span class="p">);</span></span>
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1005
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<pre style="margin: 0;">-<span id="LC1005" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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1006
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<pre style="margin: 0;">-<span id="LC1006" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">ctfGFF_cdslen</span><span class="p">:</span></span>
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1007
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<pre style="margin: 0;">-<span id="LC1007" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">g</span><span class="p">.</span><span class="n" style="color: #333;">hasCDS</span><span class="p">())</span> <span class="p">{</span></span>
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1008
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<pre style="margin: 0;">-<span id="LC1008" class="line" lang="cpp"> <span class="n" style="color: #333;">GVec</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">GffExon</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">cds</span><span class="p">;</span></span>
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1009
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<pre style="margin: 0;">-<span id="LC1009" class="line" lang="cpp"> <span class="n" style="color: #333;">g</span><span class="p">.</span><span class="n" style="color: #333;">getCDSegs</span><span class="p">(</span><span class="n" style="color: #333;">cds</span><span class="p">);</span></span>
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1010
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<pre style="margin: 0;">-<span id="LC1010" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">clen</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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1011
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<pre style="margin: 0;">-<span id="LC1011" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">x</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;">x</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">cds</span><span class="p">.</span><span class="n" style="color: #333;">Count</span><span class="p">();</span><span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>
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1012
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<pre style="margin: 0;">-<span id="LC1012" class="line" lang="cpp"> <span class="n" style="color: #333;">clen</span><span class="o" style="font-weight: 600;">+=</span><span class="n" style="color: #333;">cds</span><span class="p">[</span><span class="n" style="color: #333;">x</span><span class="p">].</span><span class="n" style="color: #333;">end</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">cds</span><span class="p">[</span><span class="n" style="color: #333;">x</span><span class="p">].</span><span class="n" style="color: #333;">start</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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1013
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<td class="diff-line-num new_line old" data-linenumber="1011" 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="LC1013" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">,</span> <span class="s" style="color: #d14;">"%d"</span><span class="p">,</span> <span class="n" style="color: #333;">clen</span><span class="p">);</span></span>
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1014
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<pre style="margin: 0;">-<span id="LC1014" class="line" lang="cpp"> <span class="p">}</span></span>
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1015
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<pre style="margin: 0;">-<span id="LC1015" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">,</span> <span class="s" style="color: #d14;">"0"</span><span class="p">);</span></span>
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1016
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<pre style="margin: 0;">-<span id="LC1016" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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1017
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<td class="diff-line-num new_line old" data-linenumber="1011" 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="LC1017" class="line" lang="cpp"> <span class="p">}</span></span>
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1018
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<td class="diff-line-num new_line old" data-linenumber="1011" 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="LC1018" class="line" lang="cpp"> <span class="p">}</span></span>
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1019
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<td class="diff-line-num new_line old" data-linenumber="1011" 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="LC1019" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">,</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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1020
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<pre style="margin: 0;">-<span id="LC1020" class="line" lang="cpp"><span class="p">}</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1021" 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">
1021
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<td class="diff-line-num new_line old" data-linenumber="1011" 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="LC1021" class="line" lang="cpp"></span>
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1022
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1011
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<pre style="margin: 0;"> <span id="LC1011" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">printAsTable</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">FILE</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">f</span><span class="p">,</span> <span class="n" style="color: #333;">GffObj</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">gfo</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">out_counter</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">NULL</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="1023" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1023
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1012
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<pre style="margin: 0;"> <span id="LC1012" class="line" lang="cpp"> <span class="n" style="color: #333;">GffObj</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">t</span><span class="o" style="font-weight: 600;">=*</span><span class="n" style="color: #333;">gfo</span><span class="p">;</span></span>
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1024
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1013
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<pre style="margin: 0;"> <span id="LC1013" class="line" lang="cpp"> <span class="n" style="color: #333;">GTData</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">tdata</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="n" style="color: #333;">GTData</span><span class="o" style="font-weight: 600;">*</span><span class="p">)(</span><span class="n" style="color: #333;">t</span><span class="p">.</span><span class="n" style="color: #333;">uptr</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1032" style="width: 35px; color: rgba(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="1021" style="width: 35px; color: rgba(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">@@ -1032,10 +1021,10 @@ void printAsTable(FILE* f, GffObj* gfo, int* out_counter=NULL) {</td>
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1032
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<td class="diff-line-num new_line" data-linenumber="1021" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1021
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<pre style="margin: 0;"> <span id="LC1021" class="line" lang="cpp"> <span class="n" style="color: #333;">pdata</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">geneinfo</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">finalize</span><span class="p">();</span></span>
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<td class="diff-line-num old_line" data-linenumber="1033" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1033
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<td class="diff-line-num new_line" data-linenumber="1022" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1022
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<pre style="margin: 0;"> <span id="LC1022" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//t.parent->addAttr("locus", locname.chars());</span></span>
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<td class="diff-line-num old_line" data-linenumber="1034" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1034
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<td class="diff-line-num new_line" data-linenumber="1023" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1023
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<pre style="margin: 0;"> <span id="LC1023" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//(*out_counter)++; ?</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1035" 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">
1035
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<td class="diff-line-num new_line old" data-linenumber="1024" 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="LC1035" class="line" lang="cpp"> <span class="n" style="color: #333;">print<span class="idiff left right">GxfTab</span></span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">t</span><span class="p">.</span><span class="n" style="color: #333;">parent</span><span class="p">);</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1036" style="width: 35px; color: rgba(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="1024" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1024
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<pre style="margin: 0;">+<span id="LC1024" class="line" lang="cpp"> <span class="n" style="color: #333;">print<span class="idiff left right">TableData</span></span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">t</span><span class="p">.</span><span class="n" style="color: #333;">parent</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="1036" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1036
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<td class="diff-line-num new_line" data-linenumber="1025" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1025
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<pre style="margin: 0;"> <span id="LC1025" class="line" lang="cpp"> <span class="n" style="color: #333;">T_NO_PRINT</span><span class="p">(</span><span class="n" style="color: #333;">t</span><span class="p">.</span><span class="n" style="color: #333;">parent</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">udata</span><span class="p">);</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1037" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1037
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<td class="diff-line-num new_line" data-linenumber="1026" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1026
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<pre style="margin: 0;"> <span id="LC1026" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1038" 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">
1038
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<td class="diff-line-num new_line old" data-linenumber="1027" 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="LC1038" class="line" lang="cpp"> <span class="n" style="color: #333;">print<span class="idiff left right">GxfTab</span></span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">gfo</span><span class="p">);</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1039" style="width: 35px; color: rgba(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="1027" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1027
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<pre style="margin: 0;">+<span id="LC1027" class="line" lang="cpp"> <span class="n" style="color: #333;">print<span class="idiff left right">TableData</span></span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">gfo</span><span class="p">);</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1039" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1039
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1028
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<pre style="margin: 0;"> <span id="LC1028" class="line" lang="cpp"><span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="1040" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1040
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<td class="diff-line-num new_line" data-linenumber="1029" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1029
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<pre style="margin: 0;"> <span id="LC1029" class="line" lang="cpp"></span>
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<td class="diff-line-num old_line" data-linenumber="1041" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1041
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<td class="diff-line-num new_line" data-linenumber="1030" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1030
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<pre style="margin: 0;"> <span id="LC1030" class="line" lang="cpp"><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 class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1423" style="width: 35px; color: rgba(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="1412" style="width: 35px; color: rgba(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">@@ -1423,7 +1412,7 @@ int main(int argc, char* argv[]) {</td>
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1423
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<td class="diff-line-num new_line" data-linenumber="1412" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1412
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<pre style="margin: 0;"> <span id="LC1412" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">firstGSeqHeader</span><span class="p">)</span> <span class="p">{</span> <span class="n" style="color: #333;">printGSeqHeader</span><span class="p">(</span><span class="n" style="color: #333;">f_out</span><span class="p">,</span> <span class="n" style="color: #333;">gdata</span><span class="p">);</span> <span class="n" style="color: #333;">firstGSeqHeader</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">false</span><span class="p">;</span> <span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="1424" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1424
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<td class="diff-line-num new_line" data-linenumber="1413" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1413
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<pre style="margin: 0;"> <span id="LC1413" class="line" lang="cpp"> <span class="n" style="color: #333;">gfst</span><span class="p">.</span><span class="n" style="color: #333;">printGxf</span><span class="p">(</span><span class="n" style="color: #333;">f_out</span><span class="p">,</span> <span class="n" style="color: #333;">exonPrinting</span><span class="p">,</span> <span class="n" style="color: #333;">tracklabel</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="n" style="color: #333;">decodeChars</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="1425" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1425
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<td class="diff-line-num new_line" data-linenumber="1414" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1414
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<pre style="margin: 0;"> <span id="LC1414" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1426" 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">
1426
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<td class="diff-line-num new_line old" data-linenumber="1415" 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="LC1426" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">print<span class="idiff left right">GxfTab</span></span><span class="p">(</span><span class="n" style="color: #333;">f_out</span><span class="p">,</span> <span class="n" style="color: #333;">gfst</span><span class="p">);</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1427" style="width: 35px; color: rgba(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="1415" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1415
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<pre style="margin: 0;">+<span id="LC1415" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">print<span class="idiff left right">TableData</span></span><span class="p">(</span><span class="n" style="color: #333;">f_out</span><span class="p">,</span> <span class="n" style="color: #333;">gfst</span><span class="p">);</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1427" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1427
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<td class="diff-line-num new_line" data-linenumber="1416" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1416
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<pre style="margin: 0;"> <span id="LC1416" class="line" lang="cpp"> <span class="p">}</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1428" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1428
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<td class="diff-line-num new_line" data-linenumber="1417" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1417
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<pre style="margin: 0;"> <span id="LC1417" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">gfs_i</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="1429" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1429
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<td class="diff-line-num new_line" data-linenumber="1418" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1418
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<pre style="margin: 0;"> <span id="LC1418" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1448" style="width: 35px; color: rgba(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="1437" style="width: 35px; color: rgba(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">@@ -1448,13 +1437,13 @@ int main(int argc, char* argv[]) {</td>
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1448
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<td class="diff-line-num new_line" data-linenumber="1437" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1437
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<pre style="margin: 0;"> <span id="LC1437" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">pdata</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">pdata</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">geneinfo</span><span class="o" style="font-weight: 600;">!=</span><span class="nb" style="color: #0086b3;">NULL</span><span class="p">)</span></span>
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<td class="diff-line-num old_line" data-linenumber="1449" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1449
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<td class="diff-line-num new_line" data-linenumber="1438" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1438
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<pre style="margin: 0;"> <span id="LC1438" class="line" lang="cpp"> <span class="n" style="color: #333;">pdata</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">geneinfo</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">finalize</span><span class="p">();</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1450" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1450
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<td class="diff-line-num new_line" data-linenumber="1439" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1439
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<pre style="margin: 0;"> <span id="LC1439" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">fmtTable</span><span class="p">)</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1451" 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">
1451
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<td class="diff-line-num new_line old" data-linenumber="1440" 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="LC1451" class="line" lang="cpp"> <span class="n" style="color: #333;">print<span class="idiff left right">GxfTab</span></span><span class="p">(</span><span class="n" style="color: #333;">f_out</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">t</span><span class="p">.</span><span class="n" style="color: #333;">parent</span><span class="p">));</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1452" style="width: 35px; color: rgba(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="1440" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1440
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<pre style="margin: 0;">+<span id="LC1440" class="line" lang="cpp"> <span class="n" style="color: #333;">print<span class="idiff left right">TableData</span></span><span class="p">(</span><span class="n" style="color: #333;">f_out</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">t</span><span class="p">.</span><span class="n" style="color: #333;">parent</span><span class="p">));</span></span>
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<td class="diff-line-num old_line" data-linenumber="1452" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1452
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<td class="diff-line-num new_line" data-linenumber="1441" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1441
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<pre style="margin: 0;"> <span id="LC1441" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span></span>
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<td class="diff-line-num old_line" data-linenumber="1453" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1453
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<td class="diff-line-num new_line" data-linenumber="1442" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1442
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<pre style="margin: 0;"> <span id="LC1442" class="line" lang="cpp"> <span class="n" style="color: #333;">t</span><span class="p">.</span><span class="n" style="color: #333;">parent</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">printGxf</span><span class="p">(</span><span class="n" style="color: #333;">f_out</span><span class="p">,</span> <span class="n" style="color: #333;">exonPrinting</span><span class="p">,</span> <span class="n" style="color: #333;">tracklabel</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="n" style="color: #333;">decodeChars</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="1454" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1454
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<td class="diff-line-num new_line" data-linenumber="1443" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1443
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<pre style="margin: 0;"> <span id="LC1443" class="line" lang="cpp"> <span class="n" style="color: #333;">T_NO_PRINT</span><span class="p">(</span><span class="n" style="color: #333;">t</span><span class="p">.</span><span class="n" style="color: #333;">parent</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">udata</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="1455" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1455
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<td class="diff-line-num new_line" data-linenumber="1444" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1444
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<pre style="margin: 0;"> <span id="LC1444" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="1456" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1456
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<td class="diff-line-num new_line" data-linenumber="1445" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1445
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<pre style="margin: 0;"> <span id="LC1445" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">fmtTable</span><span class="p">)</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1457" 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">
1457
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<td class="diff-line-num new_line old" data-linenumber="1446" 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="LC1457" class="line" lang="cpp"> <span class="n" style="color: #333;">print<span class="idiff left right">GxfTab</span></span><span class="p">(</span><span class="n" style="color: #333;">f_out</span><span class="p">,</span> <span class="n" style="color: #333;">t</span><span class="p">);</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1458" style="width: 35px; color: rgba(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="1446" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1446
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<pre style="margin: 0;">+<span id="LC1446" class="line" lang="cpp"> <span class="n" style="color: #333;">print<span class="idiff left right">TableData</span></span><span class="p">(</span><span class="n" style="color: #333;">f_out</span><span class="p">,</span> <span class="n" style="color: #333;">t</span><span class="p">);</span></span>
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1458
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<td class="diff-line-num new_line" data-linenumber="1447" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1447
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<pre style="margin: 0;"> <span id="LC1447" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span></span>
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<td class="diff-line-num old_line" data-linenumber="1459" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1459
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<td class="diff-line-num new_line" data-linenumber="1448" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1448
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<pre style="margin: 0;"> <span id="LC1448" class="line" lang="cpp"> <span class="n" style="color: #333;">t</span><span class="p">.</span><span class="n" style="color: #333;">printGxf</span><span class="p">(</span><span class="n" style="color: #333;">f_out</span><span class="p">,</span> <span class="n" style="color: #333;">exonPrinting</span><span class="p">,</span> <span class="n" style="color: #333;">tracklabel</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="n" style="color: #333;">decodeChars</span><span class="p">);</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1460" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1460
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<td class="diff-line-num new_line" data-linenumber="1449" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1449
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<pre style="margin: 0;"> <span id="LC1449" class="line" lang="cpp"> <span class="p">}</span></span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1472" style="width: 35px; color: rgba(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="1461" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1472,7 +1461,7 @@ int main(int argc, char* argv[]) {</td>
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<td class="diff-line-num old_line" data-linenumber="1472" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1472
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<td class="diff-line-num new_line" data-linenumber="1461" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1461
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<pre style="margin: 0;"> <span id="LC1461" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">firstGSeqHeader</span><span class="p">)</span> <span class="p">{</span> <span class="n" style="color: #333;">printGSeqHeader</span><span class="p">(</span><span class="n" style="color: #333;">f_out</span><span class="p">,</span> <span class="n" style="color: #333;">gdata</span><span class="p">);</span> <span class="n" style="color: #333;">firstGSeqHeader</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">false</span><span class="p">;</span> <span class="p">}</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1473" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1473
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<td class="diff-line-num new_line" data-linenumber="1462" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1462
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1462" class="line" lang="cpp"> <span class="n" style="color: #333;">gfst</span><span class="p">.</span><span class="n" style="color: #333;">printGxf</span><span class="p">(</span><span class="n" style="color: #333;">f_out</span><span class="p">,</span> <span class="n" style="color: #333;">exonPrinting</span><span class="p">,</span> <span class="n" style="color: #333;">tracklabel</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="n" style="color: #333;">decodeChars</span><span class="p">);</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1474" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1474
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<td class="diff-line-num new_line" data-linenumber="1463" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1463
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<pre style="margin: 0;"> <span id="LC1463" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1475" 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">
1475
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<pre style="margin: 0;">-<span id="LC1475" class="line" lang="cpp"> <span class="n" style="color: #333;">print<span class="idiff left right">GxfTab</span></span><span class="p">(</span><span class="n" style="color: #333;">f_out</span><span class="p">,</span> <span class="n" style="color: #333;">gfst</span><span class="p">);</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1476" style="width: 35px; color: rgba(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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1464
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<pre style="margin: 0;">+<span id="LC1464" class="line" lang="cpp"> <span class="n" style="color: #333;">print<span class="idiff left right">TableData</span></span><span class="p">(</span><span class="n" style="color: #333;">f_out</span><span class="p">,</span> <span class="n" style="color: #333;">gfst</span><span class="p">);</span></span>
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1476
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<td class="diff-line-num new_line" data-linenumber="1465" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1465
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<pre style="margin: 0;"> <span id="LC1465" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="1477" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1477
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<td class="diff-line-num new_line" data-linenumber="1466" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1466
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<pre style="margin: 0;"> <span id="LC1466" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">gfs_i</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="1478" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1478
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1467
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<pre style="margin: 0;"> <span id="LC1467" class="line" lang="cpp"> <span class="p">}</span></span>
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