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<h3>
Andreas Tille pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/gffread">Debian Med / gffread</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/gffread/-/commit/8f84d6a4137aa1f105b971864eb5ea314c617754">8f84d6a4</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2021-01-17T18:02:18+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 0.12.4</pre>
</li>
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<h4>6 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#836efb6e25a091dcb4ff8e1dbb2f0be6a5cbf14c">
Makefile
</a>
</li>
<li class="file-stats">
<a href="#2e62d67be9b972fb94be4079924f65c3df9a24ac">
gff_utils.cpp
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</li>
<li class="file-stats">
<a href="#70793cbfea41a48621c826d9f427c35d8ef91e5f">
gff_utils.h
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<li class="file-stats">
<a href="#037bd3173d312d85c9ae5e3fa8f48a79706aa6fb">
gffread.cpp
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<li class="file-stats">
<a href="#ad76bfab75291d38945f9d9d0587235d3770a87c">
prep_source.sh
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</li>
<li class="file-stats">
<a href="#27ed1fc8ed3b072a62b0853848a75e935f58075b">
tag_git.sh
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</li>
</ul>
<h4>Changes:</h4>
<li id="836efb6e25a091dcb4ff8e1dbb2f0be6a5cbf14c">
<a href="https://salsa.debian.org/med-team/gffread/-/commit/8f84d6a4137aa1f105b971864eb5ea314c617754#836efb6e25a091dcb4ff8e1dbb2f0be6a5cbf14c"><strong>Makefile</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="11" style="width: 35px; color: rgba(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">@@ -11,7 +11,7 @@ LDFLAGS := $(if $(LDFLAGS),$(LDFLAGS),-g)</td>
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<td class="diff-line-num old_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="make"></span>
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<td class="diff-line-num old_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
12
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<td class="diff-line-num new_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="make"><span class="nv" style="color: #008080;">BASEFLAGS</span> <span class="o" style="font-weight: 600;">:=</span> <span class="nt" style="color: #000080;">-Wall</span> <span class="nt" style="color: #000080;">-Wextra</span> <span class="nv" style="color: #008080;">${SEARCHDIRS}</span> <span class="nt" style="color: #000080;">-D_FILE_OFFSET_BITS</span><span class="o" style="font-weight: 600;">=</span>64 <span class="se" style="color: #d14;">\</span></span>
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<td class="diff-line-num old_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
13
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<td class="diff-line-num new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
13
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="make"><span class="nt" style="color: #000080;">-D_LARGEFILE_SOURCE</span> <span class="nt" style="color: #000080;">-D_REENTRANT</span> <span class="nt" style="color: #000080;">-fno-strict-aliasing</span> <span class="se" style="color: #d14;">\</span></span>
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<td class="diff-line-num old old_line" data-linenumber="14" 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">
14
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="make"> <span class="nt" style="color: #000080;">-std</span><span class="o" style="font-weight: 600;">=</span>c++<span class="idiff left right">0x</span> <span class="nt" style="color: #000080;">-fno-exceptions</span> <span class="nt" style="color: #000080;">-fno-rtti</span></span>
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<td class="diff-line-num new old_line" data-linenumber="15" style="width: 35px; color: rgba(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="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="make"> <span class="nt" style="color: #000080;">-std</span><span class="o" style="font-weight: 600;">=</span>c++<span class="idiff left right">11</span> <span class="nt" style="color: #000080;">-fno-exceptions</span> <span class="nt" style="color: #000080;">-fno-rtti</span></span>
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<td class="diff-line-num 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">
15
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15
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="make"></span>
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16
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<td class="diff-line-num new_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="make"><span class="nv" style="color: #008080;">GCCV8</span> <span class="o" style="font-weight: 600;">:=</span> <span class="nf" style="color: #900; font-weight: 600;">$(</span><span class="nb" style="color: #0086b3;">shell</span> <span class="nb" style="color: #0086b3;">expr</span> <span class="sb" style="color: #d14;">`</span><span class="nv" style="color: #008080;">${CXX}</span> <span class="nt" style="color: #000080;">-dumpversion</span> | <span class="nb" style="color: #0086b3;">cut</span> <span class="nt" style="color: #000080;">-f1</span> <span class="nt" style="color: #000080;">-d</span>.<span class="sb" style="color: #d14;">`</span> <span class="se" style="color: #d14;">\></span><span class="o" style="font-weight: 600;">=</span> 8<span class="nf" style="color: #900; font-weight: 600;">)</span></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="make"><span class="k" style="font-weight: 600;">ifeq</span> <span class="nv" style="color: #008080;">"$(GCCV8)" "1"</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="83" style="width: 35px; color: rgba(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="83" style="width: 35px; color: rgba(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">@@ -83,7 +83,7 @@ all release debug memcheck memdebug profile gprof prof: ../gclib gffread</td>
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<td class="diff-line-num old_line" data-linenumber="83" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="make"><span class="nl">$(OBJS) </span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">$(GCLDIR)/GBase.h $(GCLDIR)/gff.h</span></span>
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<td class="diff-line-num old_line" data-linenumber="84" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="make"><span class="nl">gffread.o </span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">gff_utils.h $(GCLDIR)/GBase.h $(GCLDIR)/gff.h</span></span>
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="make"><span class="nl">gff_utils.o </span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">gff_utils.h $(GCLDIR)/gff.h</span></span>
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<td class="diff-line-num old old_line" data-linenumber="86" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC86" class="line" lang="make"><span class="nl">${GCLDIR}/gff.o </span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">${GCLDIR}/gff.h ${GCLDIR}/GFaSeqGet.h ${GCLDIR}/GList.hh<span class="idiff left right"> ${GCLDIR}/GHash.hh</span></span></span>
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="make"><span class="nl">${GCLDIR}/gff.o </span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">${GCLDIR}/gff.h ${GCLDIR}/GFaSeqGet.h ${GCLDIR}/GList.hh</span></span>
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87
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<pre style="margin: 0;"> <span id="LC87" class="line" lang="make"><span class="nl">${GCLDIR}/GFaSeqGet.o </span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">${GCLDIR}/GFaSeqGet.h</span></span>
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="make"><span class="nl">gffread</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">$(OBJS) gffread.o</span></span>
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<pre style="margin: 0;"> <span id="LC89" class="line" lang="make"> <span class="nv" style="color: #008080;">${LINKER}</span> <span class="nv" style="color: #008080;">${LDFLAGS}</span> <span class="nt" style="color: #000080;">-o</span> <span class="nv" style="color: #008080;">$@</span> <span class="nf" style="color: #900; font-weight: 600;">${</span><span class="nb" style="color: #0086b3;">filter-out</span> %.a %.so, <span class="nv" style="color: #008080;">$^</span><span class="nf" style="color: #900; font-weight: 600;">}</span> <span class="nv" style="color: #008080;">${LIBS}</span></span>
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<li id="2e62d67be9b972fb94be4079924f65c3df9a24ac">
<a href="https://salsa.debian.org/med-team/gffread/-/commit/8f84d6a4137aa1f105b971864eb5ea314c617754#2e62d67be9b972fb94be4079924f65c3df9a24ac"><strong>gff_utils.cpp</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "gff_utils.h"</span></span>
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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="n" style="color: #333;">GHash</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;">gene_ids</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="cpp"><span class="n" style="color: #333;">GHash</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 class="idiff left right">*</span>></span> <span class="n" style="color: #333;">gene_ids</span><span class="p">;</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="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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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">debugMode</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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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -14,9 +14,13 @@ int wPadding = 0; //padding for -w option</td>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="cpp"><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_x</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">//writing fasta with spliced CDS</span></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="cpp"><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_y</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">//wrting fasta with translated CDS</span></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="cpp"><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_j</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">//wrting junctions (intron coordinates)</span></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">maxintron</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">999000000</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="cpp"><span class="n" style="color: #333;">ID_Flt_Type</span> <span class="n" style="color: #333;">IDflt</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">idFlt_None</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">TFilters</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="LC24" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">wCDSonly</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="LC25" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">wNConly</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="LC26" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">minLen</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;">//minimum transcript length</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="45" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -45,6 +49,7 @@ uint rfltEnd=MAX_UINT;</td>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">rfltWithin</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;">//check for full containment within given range</span></span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">addDescr</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="LC51" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">wfaNoCDS</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="LC53" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">fmtGFF3</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">true</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">//default output: GFF3</span></span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//other formats only make sense in transcriptOnly mode</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">@@ -57,9 +62,12 @@ GffPrintMode exonPrinting=pgffAny;</td>
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="cpp"><span class="n" style="color: #333;">GFastaDb</span> <span class="n" style="color: #333;">gfasta</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="cpp"><span class="n" style="color: #333;">GHash</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">SeqInfo</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">seqinfo</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="cpp"><span class="n" style="color: #333;">GHash</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">SeqInfo</span><span class="o" style="font-weight: 600;"><span class="idiff left right">*</span>></span> <span class="n" style="color: #333;">seqinfo</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC66" 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;">CTableField</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">tableCols</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="cpp"><span class="n" style="color: #333;">GHash</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">RefTran</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">reftbl</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="cpp"><span class="n" style="color: #333;">GHash</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">RefTran</span><span class="o" style="font-weight: 600;">*></span> <span class="n" style="color: #333;">reftbl</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="cpp"><span class="n" style="color: #333;">GStrSet</span><span class="o" style="font-weight: 600;"><></span> <span class="n" style="color: #333;">fltIDs</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="cpp"><span class="n" style="color: #333;">GStrSet</span><span class="o" style="font-weight: 600;"><></span> <span class="n" style="color: #333;">attrList</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="cpp"><span class="n" style="color: #333;">GHash</span><span class="o" style="font-weight: 600;"><</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;">isoCounter</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">//counts the valid isoforms</span></span>
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="cpp"></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">@@ -353,7 +361,27 @@ void printTableData(FILE* f, GffObj& g, bool inFasta) {</td>
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<pre style="margin: 0;"> <span id="LC361" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC362" 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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363
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<pre style="margin: 0;"> <span id="LC363" class="line" lang="cpp"><span class="p">}</span></span>
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364
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<pre style="margin: 0;">+<span id="LC364" class="line" lang="cpp"></span>
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356
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365
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<pre style="margin: 0;"> <span id="LC365" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">GffLoader</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">validateGffRec</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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366
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<pre style="margin: 0;">+<span id="LC366" 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;">checkFilters</span><span class="p">(</span><span class="n" style="color: #333;">gffrec</span><span class="p">))</span> <span class="p">{</span></span>
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367
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<pre style="margin: 0;">+<span id="LC367" 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="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">isTranscript</span><span class="p">())</span> <span class="p">{</span></span>
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368
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<pre style="margin: 0;">+<span id="LC368" class="line" lang="cpp"> <span class="n" style="color: #333;">TFilters</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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369
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<pre style="margin: 0;">+<span id="LC369" 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="o" style="font-weight: 600;">-></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;">keepGenes</span><span class="p">)</span> <span class="p">{</span></span>
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370
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<pre style="margin: 0;">+<span id="LC370" class="line" lang="cpp"> <span class="n" style="color: #333;">GPVec</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">GffObj</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">pchildren</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">gffrec</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">parent</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">children</span><span class="p">;</span></span>
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371
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<pre style="margin: 0;">+<span id="LC371" 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;">c</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;">c</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">pchildren</span><span class="p">.</span><span class="n" style="color: #333;">Count</span><span class="p">();</span><span class="n" style="color: #333;">c</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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372
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<pre style="margin: 0;">+<span id="LC372" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">pchildren</span><span class="p">[</span><span class="n" style="color: #333;">c</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="p">{</span></span>
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373
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<pre style="margin: 0;">+<span id="LC373" class="line" lang="cpp"> <span class="n" style="color: #333;">pchildren</span><span class="p">.</span><span class="n" style="color: #333;">Delete</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">);</span></span>
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374
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<pre style="margin: 0;">+<span id="LC374" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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375
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<pre style="margin: 0;">+<span id="LC375" class="line" lang="cpp"> <span class="p">}</span></span>
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376
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<pre style="margin: 0;">+<span id="LC376" class="line" lang="cpp"> <span class="p">}</span></span>
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377
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<pre style="margin: 0;">+<span id="LC377" class="line" lang="cpp"> <span class="p">}</span></span>
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378
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<pre style="margin: 0;">+<span id="LC378" class="line" lang="cpp"> <span class="p">}</span></span>
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379
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<pre style="margin: 0;">+<span id="LC379" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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380
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<pre style="margin: 0;">+<span id="LC380" class="line" lang="cpp"> <span class="p">}</span> <span class="c1" style="color: #998; font-style: italic;">//transcript rejected</span></span>
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381
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<pre style="margin: 0;">+<span id="LC381" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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382
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<pre style="margin: 0;">+<span id="LC382" class="line" lang="cpp"><span class="p">}</span></span>
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383
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<pre style="margin: 0;">+<span id="LC383" class="line" lang="cpp"></span>
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384
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<pre style="margin: 0;">+<span id="LC384" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">GffLoader</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">checkFilters</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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357
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385
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<pre style="margin: 0;"> <span id="LC385" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">reftbl</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 class="c1" style="color: #998; font-style: italic;">//check if we need to reject by ref seq filter</span></span>
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358
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386
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<pre style="margin: 0;"> <span id="LC386" class="line" lang="cpp"> <span class="n" style="color: #333;">GStr</span> <span class="n" style="color: #333;">refname</span><span class="p">(</span><span class="n" style="color: #333;">gffrec</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getRefName</span><span class="p">());</span></span>
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359
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387
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<pre style="margin: 0;"> <span id="LC387" class="line" lang="cpp"> <span class="n" style="color: #333;">RefTran</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">rt</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">reftbl</span><span class="p">.</span><span class="n" style="color: #333;">Find</span><span class="p">(</span><span class="n" style="color: #333;">refname</span><span class="p">.</span><span class="n" style="color: #333;">chars</span><span class="p">());</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="379" style="width: 35px; color: rgba(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="407" style="width: 35px; color: rgba(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">@@ -379,6 +407,12 @@ bool GffLoader::validateGffRec(GffObj* gffrec) {</td>
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379
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407
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<pre style="margin: 0;"> <span id="LC407" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//GMessage("Warning: discarding %s GFF generic gene/locus container %s\n",gffrec->getID());</span></span>
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380
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408
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<pre style="margin: 0;"> <span id="LC408" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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381
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409
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<pre style="margin: 0;"> <span id="LC409" class="line" lang="cpp"> <span class="p">}</span></span>
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410
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<pre style="margin: 0;">+<span id="LC410" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">IDflt</span><span class="p">)</span> <span class="p">{</span></span>
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411
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<pre style="margin: 0;">+<span id="LC411" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">fltIDs</span><span class="p">.</span><span class="n" style="color: #333;">hasKey</span><span class="p">(</span><span class="n" style="color: #333;">gffrec</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getID</span><span class="p">()))</span> <span class="p">{</span></span>
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412
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<pre style="margin: 0;">+<span id="LC412" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">IDflt</span><span class="o" style="font-weight: 600;">==</span><span class="n" style="color: #333;">idFlt_Exclude</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>
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413
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<pre style="margin: 0;">+<span id="LC413" class="line" lang="cpp"> <span class="p">}</span></span>
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414
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<pre style="margin: 0;">+<span id="LC414" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">IDflt</span><span class="o" style="font-weight: 600;">==</span><span class="n" style="color: #333;">idFlt_Only</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>
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415
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<pre style="margin: 0;">+<span id="LC415" class="line" lang="cpp"> <span class="p">}</span></span>
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382
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416
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<pre style="margin: 0;"> <span id="LC416" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">minLen</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;">gffrec</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">covlen</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">minLen</span><span class="p">)</span> <span class="p">{</span></span>
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383
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417
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<pre style="margin: 0;"> <span id="LC417" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">verbose</span><span class="p">)</span></span>
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384
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418
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<pre style="margin: 0;"> <span id="LC418" class="line" lang="cpp"> <span class="n" style="color: #333;">GMessage</span><span class="p">(</span><span class="s" style="color: #d14;">"Info: %s discarded due to minimum length threshold %d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="406" style="width: 35px; color: rgba(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="440" style="width: 35px; color: rgba(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">@@ -406,13 +440,22 @@ bool GffLoader::validateGffRec(GffObj* gffrec) {</td>
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406
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440
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<pre style="margin: 0;"> <span id="LC440" class="line" lang="cpp"> <span class="p">}</span></span>
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407
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441
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<pre style="margin: 0;"> <span id="LC441" class="line" lang="cpp"> <span class="p">}</span></span>
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408
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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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409
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<pre style="margin: 0;">-<span id="LC409" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">multiExon</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">gffrec</span><span class="o" style="font-weight: 600;">-></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;">1</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC410" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC411" class="line" lang="cpp"> <span class="p">}</span></span>
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412
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<pre style="margin: 0;">-<span id="LC412" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">wCDSonly</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">gffrec</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">CDstart</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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413
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<pre style="margin: 0;">-<span id="LC413" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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443
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<pre style="margin: 0;">+<span id="LC443" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">attrsFilter</span><span class="p">)</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">//mostly relevant for transcripts and gene records</span></span>
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444
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<pre style="margin: 0;">+<span id="LC444" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//remove attributes that are not in attrList</span></span>
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445
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<pre style="margin: 0;">+<span id="LC445" class="line" lang="cpp"> <span class="n" style="color: #333;">gffrec</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">removeAttrs</span><span class="p">(</span><span class="n" style="color: #333;">attrList</span><span class="p">);</span></span>
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414
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<pre style="margin: 0;"> <span id="LC446" class="line" lang="cpp"> <span class="p">}</span></span>
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415
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<pre style="margin: 0;">-<span id="LC415" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">wNConly</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">gffrec</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">hasCDS</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>
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447
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<pre style="margin: 0;">+<span id="LC447" class="line" lang="cpp"></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;">gffrec</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">isTranscript</span><span class="p">())</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">// && TFilters) ?</span></span>
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449
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<pre style="margin: 0;">+<span id="LC449" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//these filters only apply to transcripts</span></span>
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450
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<pre style="margin: 0;">+<span id="LC450" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">multiExon</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">gffrec</span><span class="o" style="font-weight: 600;">-></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;">1</span><span class="p">)</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="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">false</span><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="p">}</span></span>
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453
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<pre style="margin: 0;">+<span id="LC453" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">wCDSonly</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">gffrec</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">CDstart</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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454
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<pre style="margin: 0;">+<span id="LC454" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">false</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="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="456" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
456
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<pre style="margin: 0;">+<span id="LC456" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">wNConly</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">gffrec</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">hasCDS</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>
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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;">return</span> <span class="n" style="color: #333;">process_transcript</span><span class="p">(</span><span class="n" style="color: #333;">gfasta</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>
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<pre style="margin: 0;">+<span id="LC458" class="line" lang="cpp"> <span class="p">}</span> <span class="c1" style="color: #998; font-style: italic;">//transcript filters check</span></span>
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<pre style="margin: 0;"> <span id="LC459" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC460" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC461" class="line" lang="cpp"></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">@@ -451,13 +494,13 @@ bool process_transcript(GFastaDb& gfasta, GffObj& gffrec) {</td>
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<pre style="margin: 0;"> <span id="LC494" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC495" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC496" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">gname</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">strcmp</span><span class="p">(</span><span class="n" style="color: #333;">gname</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 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="LC454" class="line" lang="cpp"> <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;">isonum</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">isoCounter</span><span class="p">.</span><span class="n" style="color: #333;">Find</span><span class="p">(</span><span class="n" style="color: #333;">gname</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC455" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">isonum</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="LC456" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">isonum</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">new</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC457" class="line" lang="cpp"><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">isoCounter</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">Add</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">gname</span></span><span class="p"><span class="idiff">,</span></span><span class="n" style="color: #333;"><span class="idiff right">isonum</span></span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC458" class="line" lang="cpp"><span class="idiff left right"> </span> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC459" class="line" lang="cpp"><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">else</span> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">isonum</span><span class="p">)</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC460" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//defline.appendfmt(" gene=%s", gname);</span></span>
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<pre style="margin: 0;">+<span id="LC497" class="line" lang="cpp"><span class="idiff left right"> </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;">isonum</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">isoCounter</span><span class="p">.</span><span class="n" style="color: #333;">Find</span><span class="p">(</span><span class="n" style="color: #333;">gname</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC498" class="line" lang="cpp"><span class="idiff left right"> </span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">isonum</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="LC499" class="line" lang="cpp"><span class="idiff left"> </span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right">//</span>isonum=new int(1);</span></span>
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<pre style="margin: 0;">+<span id="LC500" class="line" lang="cpp"><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">isoCounter</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">Add</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">gname</span></span><span class="p"><span class="idiff">,</span></span><span class="mi" style="color: #099;"><span class="idiff right">1</span></span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC501" class="line" lang="cpp"><span class="idiff left right"> </span> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC502" class="line" lang="cpp"><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">else</span> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">isonum</span><span class="p">)</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC503" class="line" lang="cpp"><span class="idiff left right"> </span> <span class="c1" style="color: #998; font-style: italic;">//defline.appendfmt(" gene=%s", gname);</span></span>
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<pre style="margin: 0;"> <span id="LC504" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC505" class="line" lang="cpp"> <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;">0</span><span class="p">;</span></span>
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463
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506
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<pre style="margin: 0;"> <span id="LC506" class="line" lang="cpp"></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="576" style="width: 35px; color: rgba(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">@@ -533,6 +576,7 @@ bool process_transcript(GFastaDb& gfasta, GffObj& gffrec) {</td>
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533
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576
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<pre style="margin: 0;"> <span id="LC576" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">phaseNum</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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534
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577
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<pre style="margin: 0;"> <span id="LC577" class="line" lang="cpp"> <span class="nl">CDS_CHECK:</span></span>
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535
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578
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<pre style="margin: 0;"> <span id="LC578" class="line" lang="cpp"> <span class="n" style="color: #333;">uint</span> <span class="n" style="color: #333;">cds_olen</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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579
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<pre style="margin: 0;">+<span id="LC579" class="line" lang="cpp"> <span class="n" style="color: #333;">inframeStop</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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536
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580
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<pre style="margin: 0;"> <span id="LC580" class="line" lang="cpp"> <span class="n" style="color: #333;">cdsnt</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;">getSpliced</span><span class="p">(</span><span class="n" style="color: #333;">faseq</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">seqlen</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">cds_olen</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">seglst</span><span class="p">,</span> <span class="n" style="color: #333;">adjustStop</span><span class="p">);</span></span>
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537
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581
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<pre style="margin: 0;"> <span id="LC581" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//if adjustStop, seqlen has the CDS+3'UTR length, but cds_olen still has the original CDS length</span></span>
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538
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582
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<pre style="margin: 0;"> <span id="LC582" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">cdsnt</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;">cdsnt</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;">'\0'</span><span class="p">)</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">//has CDS</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="694" style="width: 35px; color: rgba(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="738" style="width: 35px; color: rgba(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">@@ -694,7 +738,7 @@ bool process_transcript(GFastaDb& gfasta, GffObj& gffrec) {</td>
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694
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738
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<pre style="margin: 0;"> <span id="LC738" class="line" lang="cpp"></span>
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695
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739
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<pre style="margin: 0;"> <span id="LC739" 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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696
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740
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<pre style="margin: 0;"> <span id="LC740" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">exont</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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697
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<pre style="margin: 0;">-<span id="LC697" 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;">CDstart</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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741
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<pre style="margin: 0;">+<span id="LC741" 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">wfaNoCDS</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">gffrec</span><span class="p">.</span><span class="n" style="color: #333;">CDstart</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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698
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742
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<pre style="margin: 0;"> <span id="LC742" class="line" lang="cpp"> <span class="n" style="color: #333;">defline</span><span class="p">.</span><span class="n" style="color: #333;">appendfmt</span><span class="p">(</span><span class="s" style="color: #d14;">" CDS=%d-%d"</span><span class="p">,</span> <span class="n" style="color: #333;">cds_start</span><span class="p">,</span> <span class="n" style="color: #333;">cds_end</span><span class="p">);</span></span>
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699
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743
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<pre style="margin: 0;"> <span id="LC743" class="line" lang="cpp"> <span class="p">}</span></span>
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700
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744
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<pre style="margin: 0;"> <span id="LC744" 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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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1169" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1169,9 +1213,9 @@ void collectLocusData(GList<GenomicSeqData>& ref_data, bool covInfo) {</td>
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1169
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<pre style="margin: 0;"> <span id="LC1213" class="line" lang="cpp"> <span class="n" style="color: #333;">GenomicSeqData</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">gdata</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">ref_data</span><span class="p">[</span><span class="n" style="color: #333;">g</span><span class="p">];</span></span>
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<td class="diff-line-num old_line" data-linenumber="1170" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1170
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<td class="diff-line-num new_line" data-linenumber="1214" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1214
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<pre style="margin: 0;"> <span id="LC1214" 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;">l</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;">l</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">gdata</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">loci</span><span class="p">.</span><span class="n" style="color: #333;">Count</span><span class="p">();</span><span class="n" style="color: #333;">l</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 old_line" data-linenumber="1171" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1171
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1215
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<pre style="margin: 0;"> <span id="LC1215" class="line" lang="cpp"> <span class="n" style="color: #333;">GffLocus</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">loc</span><span class="o" style="font-weight: 600;">=*</span><span class="p">(</span><span class="n" style="color: #333;">gdata</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">loci</span><span class="p">[</span><span class="n" style="color: #333;">l</span><span class="p">]);</span></span>
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1172
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<td class="diff-line-num new_line old" data-linenumber="1216" 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="LC1172" class="line" lang="cpp"> <span class="n" style="color: #333;">GHash</span><span class="o" style="font-weight: 600;"><</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;">gnames</span><span class="p"><span class="idiff left">(</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">true</span></span><span class="p"><span class="idiff right">)</span>;</span> <span class="c1" style="color: #998; font-style: italic;">//gene names in this locus</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1173" style="width: 35px; color: rgba(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="1216" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1216
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<pre style="margin: 0;">+<span id="LC1216" class="line" lang="cpp"> <span class="n" style="color: #333;">GHash</span><span class="o" style="font-weight: 600;"><</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;">gnames</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">//gene names in this locus</span></span>
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<td class="diff-line-num old_line" data-linenumber="1173" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1173
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<td class="diff-line-num new_line" data-linenumber="1217" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1217
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<pre style="margin: 0;"> <span id="LC1217" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//GHash<int> geneids(true); //Entrez GeneID: numbers</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1174" 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">
1174
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<td class="diff-line-num new_line old" data-linenumber="1218" 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="LC1174" class="line" lang="cpp"> <span class="n" style="color: #333;">GHash</span><span class="o" style="font-weight: 600;"><</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;">geneids</span><span class="p"><span class="idiff left">(</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">true</span></span><span class="p"><span class="idiff right">)</span>;</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1175" style="width: 35px; color: rgba(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="1218" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1218
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<pre style="margin: 0;">+<span id="LC1218" class="line" lang="cpp"> <span class="n" style="color: #333;">GHash</span><span class="o" style="font-weight: 600;"><</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;">geneids</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="1175" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1175
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<td class="diff-line-num new_line" data-linenumber="1219" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1219
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<pre style="margin: 0;"> <span id="LC1219" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">fstrand</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;">rstrand</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;">ustrand</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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1176
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<td class="diff-line-num new_line" data-linenumber="1220" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1220
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<pre style="margin: 0;"> <span id="LC1220" 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;">loc</span><span class="p">.</span><span class="n" style="color: #333;">rnas</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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<td class="diff-line-num old_line" data-linenumber="1177" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1177
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<td class="diff-line-num new_line" data-linenumber="1221" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1221
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<pre style="margin: 0;"> <span id="LC1221" 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="p">(</span><span class="n" style="color: #333;">loc</span><span class="p">.</span><span class="n" style="color: #333;">rnas</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1185" style="width: 35px; color: rgba(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="1229" style="width: 35px; color: rgba(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">@@ -1185,11 +1229,14 @@ void collectLocusData(GList<GenomicSeqData>& ref_data, bool covInfo) {</td>
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1185
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<td class="diff-line-num new_line" data-linenumber="1229" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1229
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<pre style="margin: 0;"> <span id="LC1229" class="line" lang="cpp"> <span class="n" style="color: #333;">gname</span><span class="p">.</span><span class="n" style="color: #333;">upper</span><span class="p">();</span></span>
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<td class="diff-line-num old_line" data-linenumber="1186" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1186
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<td class="diff-line-num new_line" data-linenumber="1230" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1230
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<pre style="margin: 0;"> <span id="LC1230" class="line" lang="cpp"> <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;">prevg</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">gnames</span><span class="p">.</span><span class="n" style="color: #333;">Find</span><span class="p">(</span><span class="n" style="color: #333;">gname</span><span class="p">.</span><span class="n" style="color: #333;">chars</span><span class="p">());</span></span>
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<td class="diff-line-num old_line" data-linenumber="1187" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1187
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<td class="diff-line-num new_line" data-linenumber="1231" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1231
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<pre style="margin: 0;"> <span id="LC1231" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">prevg</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="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">prevg</span><span class="p">)</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1188" 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">
1188
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<td class="diff-line-num new_line old" data-linenumber="1232" 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="LC1188" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">gnames</span><span class="p">.</span><span class="n" style="color: #333;">Add</span><span class="p">(</span><span class="n" style="color: #333;">gname</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">new</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">int</span></span><span class="p"><span class="idiff">(</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff right">)</span>);</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1189" style="width: 35px; color: rgba(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="1232" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1232
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<pre style="margin: 0;">+<span id="LC1232" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">gnames</span><span class="p">.</span><span class="n" style="color: #333;">Add</span><span class="p">(</span><span class="n" style="color: #333;">gname</span><span class="p"><span class="idiff left">.</span></span><span class="n" style="color: #333;"><span class="idiff">chars</span></span><span class="p"><span class="idiff">(),</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">1</span></span><span class="p">);</span></span>
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1189
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<td class="diff-line-num new_line" data-linenumber="1233" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1233
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<pre style="margin: 0;"> <span id="LC1233" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="1190" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1190
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<td class="diff-line-num new_line" data-linenumber="1234" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1234
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<pre style="margin: 0;"> <span id="LC1234" class="line" lang="cpp"> <span class="n" style="color: #333;">GStr</span> <span class="n" style="color: #333;">geneid</span><span class="p">(</span><span class="n" style="color: #333;">t</span><span class="p">.</span><span class="n" style="color: #333;">getGeneID</span><span class="p">());</span></span>
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1191
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<pre style="margin: 0;">-<span id="LC1191" 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;">geneid</span><span class="p">.</span><span class="n" style="color: #333;">is_empty</span><span class="p">())</span></span>
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1192
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<pre style="margin: 0;">-<span id="LC1192" class="line" lang="cpp"> <span class="n" style="color: #333;">geneids</span><span class="p">.</span><span class="n" style="color: #333;">Add</span><span class="p">(</span><span class="n" style="color: #333;">geneid</span><span class="p">.</span><span class="n" style="color: #333;">chars</span><span class="p">());</span></span>
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1235
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<pre style="margin: 0;">+<span id="LC1235" 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;">geneid</span><span class="p">.</span><span class="n" style="color: #333;">is_empty</span><span class="p">())</span> <span class="p">{</span></span>
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1236
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<pre style="margin: 0;">+<span id="LC1236" class="line" lang="cpp"> <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;">prevg</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">gnames</span><span class="p">.</span><span class="n" style="color: #333;">Find</span><span class="p">(</span><span class="n" style="color: #333;">geneid</span><span class="p">.</span><span class="n" style="color: #333;">chars</span><span class="p">());</span></span>
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1237
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<pre style="margin: 0;">+<span id="LC1237" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">prevg</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="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">prevg</span><span class="p">)</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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1238
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<pre style="margin: 0;">+<span id="LC1238" class="line" lang="cpp"> <span class="n" style="color: #333;">geneids</span><span class="p">.</span><span class="n" style="color: #333;">Add</span><span class="p">(</span><span class="n" style="color: #333;">geneid</span><span class="p">.</span><span class="n" style="color: #333;">chars</span><span class="p">(),</span> <span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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1239
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<pre style="margin: 0;">+<span id="LC1239" class="line" lang="cpp"> <span class="p">}</span></span>
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1193
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1240
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<pre style="margin: 0;"> <span id="LC1240" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//parse GeneID xrefs, if any (RefSeq):</span></span>
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1194
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1241
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<pre style="margin: 0;"> <span id="LC1241" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/*</span></span>
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1195
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1242
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<pre style="margin: 0;"> <span id="LC1242" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> GStr xrefs(t.getAttr("xrefs"));</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1220" style="width: 35px; color: rgba(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="1267" style="width: 35px; color: rgba(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">@@ -1220,11 +1267,13 @@ void collectLocusData(GList<GenomicSeqData>& ref_data, bool covInfo) {</td>
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1220
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1267
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<pre style="margin: 0;"> <span id="LC1267" class="line" lang="cpp"> <span class="n" style="color: #333;">gname</span><span class="p">.</span><span class="n" style="color: #333;">upper</span><span class="p">();</span></span>
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<td class="diff-line-num old_line" data-linenumber="1221" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1221
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1268
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<pre style="margin: 0;"> <span id="LC1268" class="line" lang="cpp"> <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;">prevg</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">gnames</span><span class="p">.</span><span class="n" style="color: #333;">Find</span><span class="p">(</span><span class="n" style="color: #333;">gname</span><span class="p">.</span><span class="n" style="color: #333;">chars</span><span class="p">());</span></span>
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<td class="diff-line-num old_line" data-linenumber="1222" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1222
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1269
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<pre style="margin: 0;"> <span id="LC1269" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">prevg</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="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">prevg</span><span class="p">)</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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1223
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<td class="diff-line-num new_line old" data-linenumber="1270" 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="LC1223" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">gnames</span><span class="p">.</span><span class="n" style="color: #333;">Add</span><span class="p">(</span><span class="n" style="color: #333;">gname</span><span class="p">,</span> <span class="k" style="font-weight: 600;"><span class="idiff left">new</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">int</span></span><span class="p"><span class="idiff">(</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff right">)</span>);</span></span>
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1270
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<pre style="margin: 0;">+<span id="LC1270" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">gnames</span><span class="p">.</span><span class="n" style="color: #333;">Add</span><span class="p">(</span><span class="n" style="color: #333;">gname</span><span class="p">,</span> <span class="mi" style="color: #099;"><span class="idiff left right">1</span></span><span class="p">);</span></span>
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1224
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1271
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<pre style="margin: 0;"> <span id="LC1271" class="line" lang="cpp"> <span class="p">}</span></span>
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1225
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1272
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<pre style="margin: 0;"> <span id="LC1272" class="line" lang="cpp"> <span class="n" style="color: #333;">GStr</span> <span class="n" style="color: #333;">geneid</span><span class="p">(</span><span class="n" style="color: #333;">nt</span><span class="p">.</span><span class="n" style="color: #333;">getID</span><span class="p">());</span></span>
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1226
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1273
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<pre style="margin: 0;"> <span id="LC1273" 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;">geneid</span><span class="p">.</span><span class="n" style="color: #333;">is_empty</span><span class="p">())</span> <span class="p">{</span></span>
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1227
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<td class="diff-line-num new_line old" data-linenumber="1274" 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="LC1227" class="line" lang="cpp"> <span class="n" style="color: #333;">geneids</span><span class="p">.</span><span class="n" style="color: #333;">Add</span><span class="p">(</span><span class="n" style="color: #333;">geneid</span><span class="p">.</span><span class="n" style="color: #333;">chars</span><span class="p">(),</span> <span class="k" style="font-weight: 600;">new</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">));</span></span>
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1274
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<pre style="margin: 0;">+<span id="LC1274" class="line" lang="cpp"> <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;">prevg</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">gnames</span><span class="p">.</span><span class="n" style="color: #333;">Find</span><span class="p">(</span><span class="n" style="color: #333;">geneid</span><span class="p">.</span><span class="n" style="color: #333;">chars</span><span class="p">());</span></span>
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1275
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<pre style="margin: 0;">+<span id="LC1275" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">prevg</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="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">prevg</span><span class="p">)</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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1276
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<pre style="margin: 0;">+<span id="LC1276" class="line" lang="cpp"> <span class="n" style="color: #333;">geneids</span><span class="p">.</span><span class="n" style="color: #333;">Add</span><span class="p">(</span><span class="n" style="color: #333;">geneid</span><span class="p">.</span><span class="n" style="color: #333;">chars</span><span class="p">(),</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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1228
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1277
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<pre style="margin: 0;"> <span id="LC1277" class="line" lang="cpp"> <span class="p">}</span></span>
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1229
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1278
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<pre style="margin: 0;"> <span id="LC1278" class="line" lang="cpp"> <span class="p">}</span></span>
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1230
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1279
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<pre style="margin: 0;"> <span id="LC1279" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//parse GeneID xrefs, if any (RefSeq):</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1258" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1258,18 +1307,18 @@ void collectLocusData(GList<GenomicSeqData>& ref_data, bool covInfo) {</td>
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1258
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1307
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<pre style="margin: 0;"> <span id="LC1307" class="line" lang="cpp"> <span class="n" style="color: #333;">loc</span><span class="p">.</span><span class="n" style="color: #333;">locus_num</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">locus_num</span><span class="p">;</span></span>
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1259
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<td class="diff-line-num new_line" data-linenumber="1308" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1308
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<pre style="margin: 0;"> <span id="LC1308" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">gnames</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 class="c1" style="color: #998; font-style: italic;">//collect all gene names associated to this locus</span></span>
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1260
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1309
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<pre style="margin: 0;"> <span id="LC1309" class="line" lang="cpp"> <span class="n" style="color: #333;">gnames</span><span class="p">.</span><span class="n" style="color: #333;">startIterate</span><span class="p">();</span></span>
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1261
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<pre style="margin: 0;">-<span id="LC1261" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;"><span class="idiff left">*</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">gfreq</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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1262
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<pre style="margin: 0;">-<span id="LC1262" 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;">key</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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1263
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<pre style="margin: 0;">-<span id="LC1263" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span> <span class="p">((</span><span class="n" style="color: #333;"><span class="idiff left">gfreq</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="n" style="color: #333;"><span class="idiff">gnames</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">NextData</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff right">key</span></span><span class="p">))</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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1264
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<td class="diff-line-num new_line old" data-linenumber="1310" 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="LC1264" class="line" lang="cpp"> <span class="n" style="color: #333;">loc</span><span class="p">.</span><span class="n" style="color: #333;">gene_names</span><span class="p">.</span><span class="n" style="color: #333;">AddIfNew</span><span class="p">(</span><span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">CGeneSym</span><span class="p">(</span><span class="n" style="color: #333;">key</span><span class="p">,</span><span class="o" style="font-weight: 600;"><span class="idiff left right">*</span></span><span class="n" style="color: #333;">gfreq</span><span class="p">));</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1310" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1310
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<pre style="margin: 0;">+<span id="LC1310" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">gfreq</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="mi" style="color: #099;"><span class="idiff right">0</span></span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1311" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1311
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<pre style="margin: 0;">+<span id="LC1311" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">c<span class="idiff left">onst</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff right">c</span>har</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">key</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 new new_line" data-linenumber="1312" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1312
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<pre style="margin: 0;">+<span id="LC1312" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span> <span class="p">((</span><span class="n" style="color: #333;"><span class="idiff left">key</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="n" style="color: #333;"><span class="idiff">gnames</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">Next</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff right">gfreq</span></span><span class="p">))</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 new new_line" data-linenumber="1313" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1313
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<pre style="margin: 0;">+<span id="LC1313" class="line" lang="cpp"> <span class="n" style="color: #333;">loc</span><span class="p">.</span><span class="n" style="color: #333;">gene_names</span><span class="p">.</span><span class="n" style="color: #333;">AddIfNew</span><span class="p">(</span><span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">CGeneSym</span><span class="p">(</span><span class="n" style="color: #333;">key</span><span class="p">,</span><span class="idiff left right"> </span><span class="n" style="color: #333;">gfreq</span><span class="p">));</span></span>
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1265
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1314
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<pre style="margin: 0;"> <span id="LC1314" class="line" lang="cpp"> <span class="p">}</span></span>
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1266
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1315
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<pre style="margin: 0;"> <span id="LC1315" class="line" lang="cpp"> <span class="p">}</span> <span class="c1" style="color: #998; font-style: italic;">//added collected gene_names</span></span>
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1267
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<td class="diff-line-num new_line" data-linenumber="1316" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1316
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<pre style="margin: 0;"> <span id="LC1316" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">geneids</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 class="c1" style="color: #998; font-style: italic;">//collect all GeneIDs names associated to this locus</span></span>
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<td class="diff-line-num old_line" data-linenumber="1268" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1268
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1317
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<pre style="margin: 0;"> <span id="LC1317" class="line" lang="cpp"> <span class="n" style="color: #333;">geneids</span><span class="p">.</span><span class="n" style="color: #333;">startIterate</span><span class="p">();</span></span>
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1269
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<td class="diff-line-num new_line old" data-linenumber="1318" 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="LC1269" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;"><span class="idiff left">*</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">gfreq</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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1270
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<td class="diff-line-num new_line old" data-linenumber="1318" 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="LC1270" 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;">key</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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1271
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<td class="diff-line-num new_line old" data-linenumber="1318" 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="LC1271" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span> <span class="p">((</span><span class="n" style="color: #333;"><span class="idiff left">gfreq</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="n" style="color: #333;"><span class="idiff">geneids</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">NextData</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff right">key</span></span><span class="p">))</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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1272
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<td class="diff-line-num new_line old" data-linenumber="1318" 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="LC1272" class="line" lang="cpp"> <span class="n" style="color: #333;">loc</span><span class="p">.</span><span class="n" style="color: #333;">gene_ids</span><span class="p">.</span><span class="n" style="color: #333;">AddIfNew</span><span class="p">(</span><span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">CGeneSym</span><span class="p">(</span><span class="n" style="color: #333;">key</span><span class="p">,</span><span class="o" style="font-weight: 600;"><span class="idiff left right">*</span></span><span class="n" style="color: #333;">gfreq</span><span class="p">));</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1318" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1318
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<pre style="margin: 0;">+<span id="LC1318" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">gfreq</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="mi" style="color: #099;"><span class="idiff right">0</span></span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1319" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1319
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<pre style="margin: 0;">+<span id="LC1319" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">c<span class="idiff left">onst</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff right">c</span>har</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">key</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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1320
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<pre style="margin: 0;">+<span id="LC1320" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span> <span class="p">((</span><span class="n" style="color: #333;"><span class="idiff left">key</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="n" style="color: #333;"><span class="idiff">geneids</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">Next</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff right">gfreq</span></span><span class="p">))</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 new new_line" data-linenumber="1321" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1321
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<pre style="margin: 0;">+<span id="LC1321" class="line" lang="cpp"> <span class="n" style="color: #333;">loc</span><span class="p">.</span><span class="n" style="color: #333;">gene_ids</span><span class="p">.</span><span class="n" style="color: #333;">AddIfNew</span><span class="p">(</span><span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">CGeneSym</span><span class="p">(</span><span class="n" style="color: #333;">key</span><span class="p">,</span><span class="idiff left right"> </span><span class="n" style="color: #333;">gfreq</span><span class="p">));</span></span>
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1273
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1322
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<pre style="margin: 0;"> <span id="LC1322" class="line" lang="cpp"> <span class="p">}</span></span>
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1274
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1323
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<pre style="margin: 0;"> <span id="LC1323" class="line" lang="cpp"> <span class="p">}</span></span>
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1275
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1324
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<pre style="margin: 0;"> <span id="LC1324" class="line" lang="cpp"> <span class="p">}</span> <span class="c1" style="color: #998; font-style: italic;">//for each locus</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1311" style="width: 35px; color: rgba(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="1360" style="width: 35px; color: rgba(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">@@ -1311,6 +1360,21 @@ GenomicSeqData* getGSeqData(GList<GenomicSeqData>& seqdata, int gseq_id) {</td>
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1311
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1360
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<pre style="margin: 0;"> <span id="LC1360" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">warnPseudo</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;">m</span><span class="p">)</span> <span class="p">{</span></span>
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1312
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<td class="diff-line-num new_line" data-linenumber="1361" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1361
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<pre style="margin: 0;"> <span id="LC1361" class="line" lang="cpp"> <span class="n" style="color: #333;">GMessage</span><span class="p">(</span><span class="s" style="color: #d14;">"Info: pseudo gene/transcript record with ID=%s discarded.</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;">m</span><span class="p">.</span><span class="n" style="color: #333;">getID</span><span class="p">());</span></span>
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1313
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1362
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<pre style="margin: 0;"> <span id="LC1362" class="line" lang="cpp"><span class="p">}</span></span>
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1363
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<pre style="margin: 0;">+<span id="LC1363" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">GffLoader</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">collectIntrons</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;">t</span><span class="p">)</span> <span class="p">{</span></span>
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1364
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<pre style="margin: 0;">+<span id="LC1364" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// assume t are coming grouped by chromosome and sorted by start coordinate!</span></span>
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1365
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<pre style="margin: 0;">+<span id="LC1365" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">intronList</span><span class="p">.</span><span class="n" style="color: #333;">jlst</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="1366" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1366
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<pre style="margin: 0;">+<span id="LC1366" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">t</span><span class="p">.</span><span class="n" style="color: #333;">gseq_id</span><span class="o" style="font-weight: 600;">!=</span><span class="n" style="color: #333;">intronList</span><span class="p">.</span><span class="n" style="color: #333;">gseq_id</span> <span class="o" style="font-weight: 600;">||</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1367" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1367
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<pre style="margin: 0;">+<span id="LC1367" class="line" lang="cpp"> <span class="n" style="color: #333;">t</span><span class="p">.</span><span class="n" style="color: #333;">start</span><span class="o" style="font-weight: 600;">>=</span><span class="n" style="color: #333;">intronList</span><span class="p">.</span><span class="n" style="color: #333;">jlst</span><span class="p">.</span><span class="n" style="color: #333;">Last</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="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1368" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1368
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<pre style="margin: 0;">+<span id="LC1368" class="line" lang="cpp"> <span class="n" style="color: #333;">intronList</span><span class="p">.</span><span class="n" style="color: #333;">print</span><span class="p">(</span><span class="n" style="color: #333;">f_j</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1369" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1369
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<pre style="margin: 0;">+<span id="LC1369" class="line" lang="cpp"> <span class="n" style="color: #333;">intronList</span><span class="p">.</span><span class="n" style="color: #333;">clear</span><span class="p">();</span></span>
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1370
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<pre style="margin: 0;">+<span id="LC1370" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1371" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1371
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<pre style="margin: 0;">+<span id="LC1371" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">t</span><span class="p">.</span><span class="n" style="color: #333;">start</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">intronList</span><span class="p">.</span><span class="n" style="color: #333;">last_t_start</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1372" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1372
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<pre style="margin: 0;">+<span id="LC1372" class="line" lang="cpp"> <span class="n" style="color: #333;">GError</span><span class="p">(</span><span class="s" style="color: #d14;">"Error collectIntrons(%s) called when last_t_start was %d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1373" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1373
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<pre style="margin: 0;">+<span id="LC1373" class="line" lang="cpp"> <span class="n" style="color: #333;">t</span><span class="p">.</span><span class="n" style="color: #333;">getID</span><span class="p">(),</span> <span class="n" style="color: #333;">intronList</span><span class="p">.</span><span class="n" style="color: #333;">last_t_start</span> <span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1374" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1374
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<pre style="margin: 0;">+<span id="LC1374" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//add this transcript's introns</span></span>
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1375
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<pre style="margin: 0;">+<span id="LC1375" class="line" lang="cpp"> <span class="p">}</span></span>
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1376
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<pre style="margin: 0;">+<span id="LC1376" class="line" lang="cpp"> <span class="n" style="color: #333;">intronList</span><span class="p">.</span><span class="n" style="color: #333;">add</span><span class="p">(</span><span class="n" style="color: #333;">t</span><span class="p">);</span></span>
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1377
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<pre style="margin: 0;">+<span id="LC1377" class="line" lang="cpp"><span class="p">}</span></span>
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1314
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1378
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<pre style="margin: 0;"> <span id="LC1378" class="line" lang="cpp"></span>
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1315
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1379
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<pre style="margin: 0;"> <span id="LC1379" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">GffLoader</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">load</span><span class="p">(</span><span class="n" style="color: #333;">GList</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">GenomicSeqData</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">seqdata</span><span class="p">,</span> <span class="n" style="color: #333;">GFFCommentParser</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">gf_parsecomment</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="1316" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1316
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<td class="diff-line-num new_line" data-linenumber="1380" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1380
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<pre style="margin: 0;"> <span id="LC1380" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">f</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;">GError</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: GffLoader::load() cannot be called before ::openFile()!</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1326" style="width: 35px; color: rgba(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="1390" style="width: 35px; color: rgba(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">@@ -1326,6 +1390,7 @@ void GffLoader::load(GList<GenomicSeqData>& seqdata, GFFCommentParser* gf_parsec</td>
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1326
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1390
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<pre style="margin: 0;"> <span id="LC1390" class="line" lang="cpp"> <span class="n" style="color: #333;">gffr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">keepGenes</span><span class="p">(</span><span class="n" style="color: #333;">keepGenes</span><span class="p">);</span></span>
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1327
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<td class="diff-line-num new_line" data-linenumber="1391" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1391
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<pre style="margin: 0;"> <span id="LC1391" class="line" lang="cpp"> <span class="n" style="color: #333;">gffr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">setIgnoreLocus</span><span class="p">(</span><span class="n" style="color: #333;">ignoreLocus</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="1328" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1328
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1392
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<pre style="margin: 0;"> <span id="LC1392" class="line" lang="cpp"> <span class="n" style="color: #333;">gffr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">setRefAlphaSorted</span><span class="p">(</span><span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">sortRefsAlpha</span><span class="p">);</span></span>
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1393
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<pre style="margin: 0;">+<span id="LC1393" class="line" lang="cpp"> <span class="n" style="color: #333;">gffr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">procEnsemblID</span><span class="p">(</span><span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">ensemblProc</span><span class="p">);</span></span>
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1329
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1394
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<pre style="margin: 0;"> <span id="LC1394" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">keepGff3Comments</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">gf_parsecomment</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;">gffr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">setCommentParser</span><span class="p">(</span><span class="n" style="color: #333;">gf_parsecomment</span><span class="p">);</span></span>
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1330
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1395
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<pre style="margin: 0;"> <span id="LC1395" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">outcounter</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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1331
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1396
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<pre style="margin: 0;"> <span id="LC1396" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">streamIn</span><span class="p">)</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">//this will ignore any clustering options</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1335" style="width: 35px; color: rgba(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="1400" style="width: 35px; color: rgba(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">@@ -1335,22 +1400,27 @@ void GffLoader::load(GList<GenomicSeqData>& seqdata, GFFCommentParser* gf_parsec</td>
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1335
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1400
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<pre style="margin: 0;"> <span id="LC1400" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">delete</span> <span class="n" style="color: #333;">t</span><span class="p">;</span></span>
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1336
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1401
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<pre style="margin: 0;"> <span id="LC1401" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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1337
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1402
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<pre style="margin: 0;"> <span id="LC1402" class="line" lang="cpp"> <span class="p">}</span></span>
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1338
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<pre style="margin: 0;">-<span id="LC1338" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">process_transcript</span><span class="p">(</span><span class="n" style="color: #333;">gfasta</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="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1339" 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">
1339
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<pre style="margin: 0;">-<span id="LC1339" class="line" lang="cpp"> <span class="n" style="color: #333;">outcounter</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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1340
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<pre style="margin: 0;">-<span id="LC1340" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">f_out</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1341" 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">
1341
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<pre style="margin: 0;">-<span id="LC1341" 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="1342" 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">
1342
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<pre style="margin: 0;">-<span id="LC1342" class="line" lang="cpp"> <span class="n" style="color: #333;">printTableData</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="n" style="color: #333;">t</span><span class="p">);</span></span>
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1343
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<pre style="margin: 0;">-<span id="LC1343" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="c1" style="color: #998; font-style: italic;">//GFF3, GTF, BED, TLF</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1344" 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">
1344
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<pre style="margin: 0;">-<span id="LC1344" class="line" lang="cpp"> <span class="n" style="color: #333;">t</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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1345
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<pre style="margin: 0;">-<span id="LC1345" class="line" lang="cpp"> <span class="p">}</span></span>
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1403
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<pre style="margin: 0;">+<span id="LC1403" class="line" lang="cpp"></span>
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1404
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<pre style="margin: 0;">+<span id="LC1404" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">f_j</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;">t</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">isTranscript</span><span class="p">()</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;">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;">1</span><span class="p">)</span></span>
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1405
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<pre style="margin: 0;">+<span id="LC1405" class="line" lang="cpp"> <span class="n" style="color: #333;">collectIntrons</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>
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1406
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<pre style="margin: 0;">+<span id="LC1406" class="line" lang="cpp"></span>
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1407
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<pre style="margin: 0;">+<span id="LC1407" class="line" lang="cpp"> <span class="n" style="color: #333;">outcounter</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1408" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1408
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<pre style="margin: 0;">+<span id="LC1408" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">f_out</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1409" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1409
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<pre style="margin: 0;">+<span id="LC1409" 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 new old_line" data-linenumber="1346" style="width: 35px; color: rgba(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="1410" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1410
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<pre style="margin: 0;">+<span id="LC1410" class="line" lang="cpp"> <span class="n" style="color: #333;">printTableData</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="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="1346" style="width: 35px; color: rgba(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="1411" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1411
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<pre style="margin: 0;">+<span id="LC1411" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="c1" style="color: #998; font-style: italic;">//GFF3, GTF, BED, TLF</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1346" style="width: 35px; color: rgba(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="1412" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1412
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<pre style="margin: 0;">+<span id="LC1412" class="line" lang="cpp"> <span class="n" style="color: #333;">t</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="1346" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1346
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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="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="1347" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1347
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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="k" style="font-weight: 600;">delete</span> <span class="n" style="color: #333;">t</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="1348" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1348
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<td class="diff-line-num new_line" data-linenumber="1415" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1415
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<pre style="margin: 0;"> <span id="LC1415" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1349" style="width: 35px; color: rgba(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="1416" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1416
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<pre style="margin: 0;">+<span id="LC1416" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">f_j</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">intronList</span><span class="p">.</span><span class="n" style="color: #333;">jlst</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 old_line" data-linenumber="1349" style="width: 35px; color: rgba(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="1417" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1417
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<pre style="margin: 0;">+<span id="LC1417" class="line" lang="cpp"> <span class="n" style="color: #333;">intronList</span><span class="p">.</span><span class="n" style="color: #333;">print</span><span class="p">(</span><span class="n" style="color: #333;">f_j</span><span class="p">);</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1349" style="width: 35px; color: rgba(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="1418" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1418
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<pre style="margin: 0;">+<span id="LC1418" class="line" lang="cpp"> <span class="n" style="color: #333;">intronList</span><span class="p">.</span><span class="n" style="color: #333;">clear</span><span class="p">();</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1349" style="width: 35px; color: rgba(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="1419" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1419
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<pre style="margin: 0;">+<span id="LC1419" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="1349" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1349
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<td class="diff-line-num new_line" data-linenumber="1420" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1420
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<pre style="margin: 0;"> <span id="LC1420" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">delete</span> <span class="n" style="color: #333;">gffr</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="1350" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1350
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<td class="diff-line-num new_line" data-linenumber="1421" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1421
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<pre style="margin: 0;"> <span id="LC1421" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="1351" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1351
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<td class="diff-line-num new_line" data-linenumber="1422" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1422
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<pre style="margin: 0;"> <span id="LC1422" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="1352" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1352
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<td class="diff-line-num new_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">
1423
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<pre style="margin: 0;"> <span id="LC1423" class="line" lang="cpp"></span>
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<td class="diff-line-num old old_line" data-linenumber="1353" 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">
1353
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<td class="diff-line-num new_line old" data-linenumber="1424" 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="LC1353" class="line" lang="cpp"></span>
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<td class="diff-line-num old_line" data-linenumber="1354" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1354
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<td class="diff-line-num new_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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<pre style="margin: 0;"> <span id="LC1424" class="line" lang="cpp"> <span class="n" style="color: #333;">gffr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">readAll</span><span class="p">();</span></span>
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<td class="diff-line-num old_line" data-linenumber="1355" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1355
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<td class="diff-line-num new_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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<pre style="margin: 0;"> <span id="LC1425" class="line" lang="cpp"> <span class="n" style="color: #333;">GVec</span><span class="o" style="font-weight: 600;"><</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;">pseudoFeatureIds</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">//feature type: pseudo*</span></span>
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<td class="diff-line-num old_line" data-linenumber="1356" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1356
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<td class="diff-line-num new_line" data-linenumber="1426" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1426
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<pre style="margin: 0;"> <span id="LC1426" class="line" lang="cpp"> <span class="n" style="color: #333;">GVec</span><span class="o" style="font-weight: 600;"><</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;">pseudoAttrIds</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// attribute: [is]pseudo*=true/yes/1</span></span>
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<td class="diff-line-num unfold js-unfold old_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">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1508" style="width: 35px; color: rgba(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">@@ -1438,9 +1508,12 @@ void GffLoader::load(GList<GenomicSeqData>& seqdata, GFFCommentParser* gf_parsec</td>
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1438
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1508
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<pre style="margin: 0;"> <span id="LC1508" class="line" lang="cpp"> <span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">subftype_id</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">gff_fid_exon</span><span class="p">;</span></span>
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<td class="diff-line-num old_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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1509
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<pre style="margin: 0;"> <span id="LC1509" class="line" lang="cpp"> <span class="p">}</span></span>
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1440
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1510
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<pre style="margin: 0;"> <span id="LC1510" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//GList<GffObj> gfadd(false,false); -- for gf_validate()?</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1441" 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">
1441
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<td class="diff-line-num new_line old" data-linenumber="1511" 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="LC1441" 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;">validateGffRec</span><span class="p">(</span><span class="n" style="color: #333;">m</span><span class="p">))</span> <span class="p">{</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1442" style="width: 35px; color: rgba(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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1511
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<pre style="margin: 0;">+<span id="LC1511" 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;">validateGffRec</span><span class="p">(</span><span class="n" style="color: #333;">m</span><span class="p">))</span> <span class="p">{</span><span class="idiff left"> </span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right">//this will also apply process_transcript() CDS filters etc.</span></span></span>
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1442
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<td class="diff-line-num new_line" data-linenumber="1512" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1512
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<pre style="margin: 0;"> <span id="LC1512" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="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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<td class="diff-line-num new_line" data-linenumber="1513" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1513
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<pre style="margin: 0;"> <span id="LC1513" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1514" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1514
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<pre style="margin: 0;">+<span id="LC1514" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">f_j</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;">m</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">isTranscript</span><span class="p">()</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">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;">1</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1515" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1515
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<pre style="margin: 0;">+<span id="LC1515" class="line" lang="cpp"> <span class="n" style="color: #333;">collectIntrons</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">m</span><span class="p">);</span></span>
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1516
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<pre style="margin: 0;">+<span id="LC1516" class="line" lang="cpp"></span>
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1444
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1517
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<pre style="margin: 0;"> <span id="LC1517" class="line" lang="cpp"> <span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">isUsed</span><span class="p">(</span><span class="nb" style="color: #0086b3;">true</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">//so the gffreader won't destroy it</span></span>
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<td class="diff-line-num old_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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<td class="diff-line-num new_line" data-linenumber="1518" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1518
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<pre style="margin: 0;"> <span id="LC1518" class="line" lang="cpp"> <span class="n" style="color: #333;">GenomicSeqData</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">gdata</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">getGSeqData</span><span class="p">(</span><span class="n" style="color: #333;">seqdata</span><span class="p">,</span> <span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">gseq_id</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="1446" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1446
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<td class="diff-line-num new_line" data-linenumber="1519" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1519
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<pre style="margin: 0;"> <span id="LC1519" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">keep</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">placeGf</span><span class="p">(</span><span class="n" style="color: #333;">m</span><span class="p">,</span> <span class="n" style="color: #333;">gdata</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1523" style="width: 35px; color: rgba(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">@@ -1450,6 +1523,10 @@ void GffLoader::load(GList<GenomicSeqData>& seqdata, GFFCommentParser* gf_parsec</td>
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1450
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1523
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<pre style="margin: 0;"> <span id="LC1523" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//GMessage("Feature %s(%d-%d) is going to be discarded..\n",m->getID(), m->start, m->end);</span></span>
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<td class="diff-line-num old_line" data-linenumber="1451" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1451
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<td class="diff-line-num new_line" data-linenumber="1524" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1524
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<pre style="margin: 0;"> <span id="LC1524" class="line" lang="cpp"> <span class="p">}</span></span>
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1452
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<td class="diff-line-num new_line" data-linenumber="1525" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1525
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<pre style="margin: 0;"> <span id="LC1525" class="line" lang="cpp"> <span class="p">}</span> <span class="c1" style="color: #998; font-style: italic;">//for each read gffObj</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1453" style="width: 35px; color: rgba(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="1526" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1526
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<pre style="margin: 0;">+<span id="LC1526" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">f_j</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">intronList</span><span class="p">.</span><span class="n" style="color: #333;">jlst</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="1527" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1527
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<pre style="margin: 0;">+<span id="LC1527" class="line" lang="cpp"> <span class="n" style="color: #333;">intronList</span><span class="p">.</span><span class="n" style="color: #333;">print</span><span class="p">(</span><span class="n" style="color: #333;">f_j</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1528" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1528
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<pre style="margin: 0;">+<span id="LC1528" class="line" lang="cpp"> <span class="n" style="color: #333;">intronList</span><span class="p">.</span><span class="n" style="color: #333;">clear</span><span class="p">();</span></span>
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1529
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<pre style="margin: 0;">+<span id="LC1529" class="line" lang="cpp"> <span class="p">}</span></span>
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1453
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<td class="diff-line-num new_line" data-linenumber="1530" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1530
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<pre style="margin: 0;"> <span id="LC1530" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//if (verbose) GMessage(" .. %d records from %s clustered into loci.\n", gffr->gflst.Count(), fname.chars());</span></span>
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1454
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1531
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<pre style="margin: 0;"> <span id="LC1531" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//if (f && f!=stdin) { fclose(f); f=NULL; }</span></span>
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<pre style="margin: 0;"> <span id="LC1532" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">delete</span> <span class="n" style="color: #333;">gffr</span><span class="p">;</span></span>
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<a href="https://salsa.debian.org/med-team/gffread/-/commit/8f84d6a4137aa1f105b971864eb5ea314c617754#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">@@ -17,10 +17,26 @@ extern int wPadding; //padding for -w option</td>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="objective_c"><span class="k" style="font-weight: 600;">extern</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_x</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">//writing fasta with spliced CDS</span></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="objective_c"><span class="k" style="font-weight: 600;">extern</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_y</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">//wrting fasta with translated CDS</span></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="objective_c"></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="objective_c"><span class="k" style="font-weight: 600;">extern</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_j</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">//wrting junctions (introns)</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="objective_c"></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="objective_c"></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="objective_c"><span class="k" style="font-weight: 600;">extern</span> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">TFilters</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="objective_c"></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="objective_c"><span class="k" style="font-weight: 600;">extern</span> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">wfaNoCDS</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="objective_c"></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="objective_c"><span class="k" style="font-weight: 600;">extern</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">maxintron</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="objective_c"></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="objective_c"><span class="k" style="font-weight: 600;">extern</span> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">wCDSonly</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="objective_c"><span class="k" style="font-weight: 600;">extern</span> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">wNConly</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="objective_c"></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="objective_c"><span class="k" style="font-weight: 600;">enum</span> <span class="n" style="color: #333;">ID_Flt_Type</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="objective_c"> <span class="n" style="color: #333;">idFlt_None</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="LC34" class="line" lang="objective_c"> <span class="n" style="color: #333;">idFlt_Only</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="objective_c"> <span class="n" style="color: #333;">idFlt_Exclude</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="objective_c"><span class="p">};</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="objective_c"></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="objective_c"><span class="k" style="font-weight: 600;">extern</span> <span class="n" style="color: #333;">ID_Flt_Type</span> <span class="n" style="color: #333;">IDflt</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="objective_c"></span>
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24
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="objective_c"><span class="k" style="font-weight: 600;">extern</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">minLen</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">//minimum transcript length</span></span>
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25
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="objective_c"><span class="k" style="font-weight: 600;">extern</span> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">validCDSonly</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// translation with no in-frame STOP</span></span>
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26
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="objective_c"><span class="k" style="font-weight: 600;">extern</span> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">bothStrands</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">//for single-exon mRNA validation, check the other strand too</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">@@ -105,15 +121,14 @@ class RefTran {</td>
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<pre style="margin: 0;"> <span id="LC121" class="line" lang="objective_c"><span class="p">};</span></span>
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<pre style="margin: 0;"> <span id="LC122" class="line" lang="objective_c"></span>
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<pre style="margin: 0;"> <span id="LC123" class="line" lang="objective_c"><span class="k" style="font-weight: 600;">extern</span> <span class="n" style="color: #333;">GFastaDb</span> <span class="n" style="color: #333;">gfasta</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC108" class="line" lang="objective_c"><span class="k" style="font-weight: 600;">extern</span> <span class="n" style="color: #333;">GHash</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">SeqInfo</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">seqinfo</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="objective_c"><span class="k" style="font-weight: 600;">extern</span> <span class="n" style="color: #333;">GHash</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">SeqInfo</span><span class="o" style="font-weight: 600;"><span class="idiff left right">*</span>></span> <span class="n" style="color: #333;">seqinfo</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC125" class="line" lang="objective_c"><span class="k" style="font-weight: 600;">extern</span> <span class="n" style="color: #333;">GHash</span><span class="o" style="font-weight: 600;"><</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;">isoCounter</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">//counts the valid isoforms</span></span>
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<pre style="margin: 0;">-<span id="LC110" class="line" lang="objective_c"><span class="k" style="font-weight: 600;">extern</span> <span class="n" style="color: #333;">GHash</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">RefTran</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">reftbl</span><span class="p">;</span></span>
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126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="objective_c"><span class="k" style="font-weight: 600;">extern</span> <span class="n" style="color: #333;">GHash</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">RefTran</span><span class="o" style="font-weight: 600;"><span class="idiff left right">*</span>></span> <span class="n" style="color: #333;">reftbl</span><span class="p">;</span></span>
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111
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<pre style="margin: 0;"> <span id="LC127" class="line" lang="objective_c"></span>
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<pre style="margin: 0;"> <span id="LC128" class="line" lang="objective_c"><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="nf" style="color: #900; font-weight: 600;">getSeqDescr</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;">seqid</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC129" class="line" lang="objective_c"><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="nf" style="color: #900; font-weight: 600;">getSeqName</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;">seqid</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC130" class="line" lang="objective_c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">adjust_stopcodon</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="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">adj</span><span class="p">,</span> <span class="n" style="color: #333;">GList</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">GSeg</span><span class="o" style="font-weight: 600;">>*</span> <span class="n" style="color: #333;">seglst</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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115
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131
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<pre style="margin: 0;"> <span id="LC131" class="line" lang="objective_c"><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="n" style="color: #333;">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>
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<pre style="margin: 0;">-<span id="LC116" class="line" lang="objective_c"><span class="n" style="color: #333;">bool</span> <span class="nf" style="color: #900; font-weight: 600;">validateGffRec</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>
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<pre style="margin: 0;"> <span id="LC132" class="line" lang="objective_c"><span class="n" style="color: #333;">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>
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118
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133
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<pre style="margin: 0;"> <span id="LC133" class="line" lang="objective_c"></span>
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119
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134
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<pre style="margin: 0;"> <span id="LC134" class="line" lang="objective_c"><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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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -144,11 +159,84 @@ class CTableField {</td>
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159
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<pre style="margin: 0;"> <span id="LC159" class="line" lang="objective_c"></span>
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145
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160
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<pre style="margin: 0;"> <span id="LC160" class="line" lang="objective_c"></span>
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146
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<pre style="margin: 0;"> <span id="LC161" class="line" lang="objective_c"><span class="k" style="font-weight: 600;">extern</span> <span class="n" style="color: #333;">GVec</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">CTableField</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">tableCols</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">//table output format fields</span></span>
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="objective_c"><span class="k" style="font-weight: 600;">extern</span> <span class="n" style="color: #333;">GStrSet</span><span class="o" style="font-weight: 600;"><></span> <span class="n" style="color: #333;">attrList</span><span class="p">;</span></span>
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163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="objective_c"><span class="k" style="font-weight: 600;">extern</span> <span class="n" style="color: #333;">GStrSet</span><span class="o" style="font-weight: 600;"><></span> <span class="n" style="color: #333;">fltIDs</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC164" class="line" lang="objective_c"></span>
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<pre style="margin: 0;"> <span id="LC165" class="line" lang="objective_c"><span class="n" style="color: #333;">class</span> <span class="n" style="color: #333;">GffLocus</span><span class="p">;</span></span>
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149
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<pre style="margin: 0;"> <span id="LC166" class="line" lang="objective_c"><span class="n" style="color: #333;">class</span> <span class="n" style="color: #333;">GenomicSeqData</span><span class="p">;</span></span>
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150
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<pre style="margin: 0;"> <span id="LC167" class="line" lang="objective_c"><span class="n" style="color: #333;">class</span> <span class="n" style="color: #333;">GeneInfo</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC168" class="line" lang="objective_c"></span>
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="objective_c"><span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">CIntronData</span><span class="o" style="font-weight: 600;">:</span><span class="n" style="color: #333;">public</span> <span class="n" style="color: #333;">GSeg</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="objective_c"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">strand</span><span class="p">;</span><span class="c1" style="color: #998; font-style: italic;">//'.' < '-' < '+' (reverse ASCII order)</span></span>
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="objective_c"> <span class="n" style="color: #333;">GVec</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">GStr</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">ts</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">//list of transcript IDs sharing this intron</span></span>
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172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="objective_c"> <span class="n" style="color: #333;">CIntronData</span><span class="p">(</span><span class="n" style="color: #333;">uint</span> <span class="n" style="color: #333;">istart</span><span class="p">,</span> <span class="n" style="color: #333;">uint</span> <span class="n" style="color: #333;">iend</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">tstrand</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">t_id</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">NULL</span><span class="p">)</span><span class="o" style="font-weight: 600;">:</span><span class="n" style="color: #333;">GSeg</span><span class="p">(</span><span class="n" style="color: #333;">istart</span><span class="p">,</span> <span class="n" style="color: #333;">iend</span><span class="p">),</span></span>
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173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="objective_c"> <span class="n" style="color: #333;">strand</span><span class="p">(</span><span class="n" style="color: #333;">tstrand</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="174" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="objective_c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">t_id</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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175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="objective_c"> <span class="n" style="color: #333;">GStr</span> <span class="n" style="color: #333;">tid</span><span class="p">(</span><span class="n" style="color: #333;">t_id</span><span class="p">);</span></span>
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176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="objective_c"> <span class="n" style="color: #333;">ts</span><span class="p">.</span><span class="n" style="color: #333;">Add</span><span class="p">(</span><span class="n" style="color: #333;">tid</span><span class="p">);</span></span>
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177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="objective_c"> <span class="p">}</span></span>
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178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="objective_c"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="179" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="objective_c"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">add</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">t_id</span><span class="p">)</span> <span class="p">{</span></span>
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180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="objective_c"> <span class="n" style="color: #333;">GStr</span> <span class="n" style="color: #333;">tid</span><span class="p">(</span><span class="n" style="color: #333;">t_id</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="181" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="objective_c"> <span class="n" style="color: #333;">ts</span><span class="p">.</span><span class="n" style="color: #333;">Add</span><span class="p">(</span><span class="n" style="color: #333;">tid</span><span class="p">);</span></span>
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182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="objective_c"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="183" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="objective_c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">operator</span><span class="o" style="font-weight: 600;">==</span><span class="p">(</span><span class="n" style="color: #333;">CIntronData</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">d</span><span class="p">){</span></span>
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<td class="diff-line-num new new_line" data-linenumber="184" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
184
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="objective_c"> <span class="k" style="font-weight: 600;">return</span> <span class="p">(</span><span class="n" style="color: #333;">start</span><span class="o" style="font-weight: 600;">==</span><span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">end</span><span class="o" style="font-weight: 600;">==</span><span class="n" style="color: #333;">d</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;">strand</span><span class="o" style="font-weight: 600;">==</span><span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">strand</span><span class="p">);</span></span>
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185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="objective_c"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="186" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="objective_c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">operator</span><span class="o" style="font-weight: 600;"><</span><span class="p">(</span><span class="n" style="color: #333;">CIntronData</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">d</span><span class="p">){</span></span>
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<td class="diff-line-num new new_line" data-linenumber="187" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="objective_c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">start</span><span class="o" style="font-weight: 600;">==</span><span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">start</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="188" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
188
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="objective_c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">end</span><span class="o" style="font-weight: 600;">==</span><span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">)</span> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">strand</span><span class="o" style="font-weight: 600;">></span><span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">strand</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="189" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
189
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="objective_c"> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">return</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;">d</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">);</span></span>
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190
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="objective_c"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="191" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
191
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="objective_c"> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">return</span> <span class="p">(</span><span class="n" style="color: #333;">start</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">start</span><span class="p">);</span></span>
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192
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="objective_c"> <span class="p">}</span></span>
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193
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="objective_c"></span>
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194
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="objective_c"><span class="p">};</span></span>
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195
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="objective_c"></span>
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<td class="diff-line-num new new_line" data-linenumber="196" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
196
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="objective_c"><span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">CIntronList</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="197" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
197
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="objective_c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">gseq_id</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="198" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
198
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="objective_c"> <span class="n" style="color: #333;">uint</span> <span class="n" style="color: #333;">last_t_start</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">//just to check if input is sorted properly!</span></span>
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<td class="diff-line-num new new_line" data-linenumber="199" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
199
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="objective_c"> <span class="n" style="color: #333;">GList</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">CIntronData</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">jlst</span><span class="p">;</span></span>
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200
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="objective_c"> <span class="n" style="color: #333;">CIntronList</span><span class="p">()</span><span class="o" style="font-weight: 600;">:</span><span class="n" style="color: #333;">gseq_id</span><span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">),</span><span class="n" style="color: #333;">last_t_start</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">),</span> <span class="n" style="color: #333;">jlst</span><span class="p">(</span><span class="nb" style="color: #0086b3;">true</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">)</span> <span class="p">{}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="201" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
201
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="objective_c"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">add</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;">t</span><span class="p">)</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">//add all introns of t to jlst</span></span>
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<td class="diff-line-num new new_line" data-linenumber="202" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
202
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="objective_c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">t</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;">2</span><span class="p">)</span> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">//nothing to do</span></span>
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<td class="diff-line-num new new_line" data-linenumber="203" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
203
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="objective_c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">gseq_id</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;">gseq_id</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;">gseq_id</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="204" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
204
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="objective_c"> <span class="n" style="color: #333;">GError</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: CIntronList::add(%s) on different ref seq!</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;">t</span><span class="p">.</span><span class="n" style="color: #333;">getID</span><span class="p">());</span></span>
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205
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="objective_c"> <span class="n" style="color: #333;">gseq_id</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;">gseq_id</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="206" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
206
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="objective_c"> <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;">1</span><span class="p">;</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">t</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="n" style="color: #333;">i</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="207" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
207
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="objective_c"> <span class="n" style="color: #333;">CIntronData</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">nintr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">new</span> <span class="n" style="color: #333;">CIntronData</span><span class="p">(</span><span class="n" style="color: #333;">t</span><span class="p">.</span><span class="n" style="color: #333;">exons</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">end</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="208" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
208
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="objective_c"> <span class="n" style="color: #333;">t</span><span class="p">.</span><span class="n" style="color: #333;">exons</span><span class="p">[</span><span class="nf" style="color: #900; font-weight: 600;">i</span><span class="p">]</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">start</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">t</span><span class="p">.</span><span class="n" style="color: #333;">strand</span><span class="p">,</span> <span class="n" style="color: #333;">t</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 new new_line" data-linenumber="209" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
209
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="objective_c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">fidx</span><span class="o" style="font-weight: 600;">=-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="210" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
210
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="objective_c"> <span class="n" style="color: #333;">CIntronData</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">xintr</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">jlst</span><span class="p">.</span><span class="n" style="color: #333;">AddIfNew</span><span class="p">(</span><span class="n" style="color: #333;">nintr</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">fidx</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="211" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
211
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="objective_c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">xintr</span><span class="o" style="font-weight: 600;">!=</span><span class="n" style="color: #333;">nintr</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="212" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
212
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="objective_c"> <span class="c1" style="color: #998; font-style: italic;">//nintr already exists,it was deallocated</span></span>
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<td class="diff-line-num new new_line" data-linenumber="213" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
213
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="objective_c"> <span class="n" style="color: #333;">xintr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">add</span><span class="p">(</span><span class="n" style="color: #333;">t</span><span class="p">.</span><span class="n" style="color: #333;">getID</span><span class="p">());</span></span>
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214
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="objective_c"> <span class="p">}</span></span>
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215
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="objective_c"> <span class="n" style="color: #333;">last_t_start</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;">start</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="objective_c"> <span class="p">}</span> <span class="c1" style="color: #998; font-style: italic;">//for each intron</span></span>
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217
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="objective_c"> <span class="p">}</span></span>
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218
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="objective_c"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">clear</span><span class="p">()</span> <span class="p">{</span></span>
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219
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="objective_c"> <span class="n" style="color: #333;">gseq_id</span><span class="o" style="font-weight: 600;">=-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="objective_c"> <span class="n" style="color: #333;">last_t_start</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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221
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="objective_c"> <span class="n" style="color: #333;">jlst</span><span class="p">.</span><span class="n" style="color: #333;">Clear</span><span class="p">();</span></span>
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="objective_c"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="objective_c"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">print</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="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="objective_c"> <span class="c1" style="color: #998; font-style: italic;">//simple tab delimited format: chr, start, end, strand, transcriptIDs comma delimited</span></span>
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225
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="objective_c"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">gseqname</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">GffObj</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">names</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">gseqs</span><span class="p">.</span><span class="n" style="color: #333;">getName</span><span class="p">(</span><span class="n" style="color: #333;">gseq_id</span><span class="p">);</span></span>
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226
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="objective_c"> <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;">jlst</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="n" style="color: #333;">i</span><span class="p">)</span> <span class="p">{</span></span>
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227
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<pre style="margin: 0;">+<span id="LC227" class="line" lang="objective_c"> <span class="n" style="color: #333;">CIntronData</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">idata</span><span class="o" style="font-weight: 600;">=*</span><span class="p">(</span><span class="n" style="color: #333;">jlst</span><span class="p">[</span><span class="nf" style="color: #900; font-weight: 600;">i</span><span class="p">]);</span></span>
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228
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="objective_c"> <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;">\t</span><span class="s" style="color: #d14;">%d</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%d</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%c</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">gseqname</span><span class="p">,</span> <span class="n" style="color: #333;">idata</span><span class="p">.</span><span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="n" style="color: #333;">idata</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">,</span> <span class="n" style="color: #333;">idata</span><span class="p">.</span><span class="n" style="color: #333;">strand</span><span class="p">);</span></span>
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229
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="objective_c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">idata</span><span class="p">.</span><span class="n" style="color: #333;">ts</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;">1</span><span class="p">)</span></span>
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230
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<pre style="margin: 0;">+<span id="LC230" class="line" lang="objective_c"> <span class="n" style="color: #333;">idata</span><span class="p">.</span><span class="n" style="color: #333;">ts</span><span class="p">.</span><span class="n" style="color: #333;">Sort</span><span class="p">();</span></span>
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<td class="diff-line-num new new_line" data-linenumber="231" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
231
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<pre style="margin: 0;">+<span id="LC231" class="line" lang="objective_c"> <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;">t</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;">t</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">idata</span><span class="p">.</span><span class="n" style="color: #333;">ts</span><span class="p">.</span><span class="n" style="color: #333;">Count</span><span class="p">();</span><span class="n" style="color: #333;">t</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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232
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<pre style="margin: 0;">+<span id="LC232" class="line" lang="objective_c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">t</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;">idata</span><span class="p">.</span><span class="n" style="color: #333;">ts</span><span class="p">[</span><span class="nf" style="color: #900; font-weight: 600;">t</span><span class="p">].</span><span class="n" style="color: #333;">chars</span><span class="p">());</span></span>
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<td class="diff-line-num new new_line" data-linenumber="233" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
233
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<pre style="margin: 0;">+<span id="LC233" class="line" lang="objective_c"> <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;">"%s"</span><span class="p">,</span> <span class="n" style="color: #333;">idata</span><span class="p">.</span><span class="n" style="color: #333;">ts</span><span class="p">[</span><span class="nf" style="color: #900; font-weight: 600;">t</span><span class="p">].</span><span class="n" style="color: #333;">chars</span><span class="p">());</span></span>
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<pre style="margin: 0;">+<span id="LC234" class="line" lang="objective_c"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="objective_c"> <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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<pre style="margin: 0;">+<span id="LC236" class="line" lang="objective_c"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="objective_c"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="objective_c"><span class="p">};</span></span>
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239
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<pre style="margin: 0;">+<span id="LC239" class="line" lang="objective_c"></span>
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152
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240
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<pre style="margin: 0;"> <span id="LC240" class="line" lang="objective_c"><span class="n" style="color: #333;">class</span> <span class="n" style="color: #333;">GTData</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">// transcript associated data</span></span>
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153
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241
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<pre style="margin: 0;"> <span id="LC241" class="line" lang="objective_c"> <span class="nl">public:</span></span>
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154
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242
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<pre style="margin: 0;"> <span id="LC242" class="line" lang="objective_c"> <span class="n" style="color: #333;">GffObj</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">rna</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="662" style="width: 35px; color: rgba(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="750" style="width: 35px; color: rgba(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">@@ -662,6 +750,7 @@ class GffLoader {</td>
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662
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750
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<pre style="margin: 0;"> <span id="LC750" class="line" lang="objective_c"> <span class="n" style="color: #333;">GStr</span> <span class="n" style="color: #333;">fname</span><span class="p">;</span></span>
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663
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751
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<pre style="margin: 0;"> <span id="LC751" class="line" lang="objective_c"> <span class="kt" style="color: #458; font-weight: 600;">FILE</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">f</span><span class="p">;</span></span>
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752
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<pre style="margin: 0;"> <span id="LC752" class="line" lang="objective_c"> <span class="n" style="color: #333;">GffNames</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">names</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC753" class="line" lang="objective_c"> <span class="n" style="color: #333;">CIntronList</span> <span class="n" style="color: #333;">intronList</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// collect introns for -j output</span></span>
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665
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754
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<pre style="margin: 0;"> <span id="LC754" class="line" lang="objective_c"> <span class="k" style="font-weight: 600;">union</span> <span class="p">{</span></span>
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755
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<pre style="margin: 0;"> <span id="LC755" class="line" lang="objective_c"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">options</span><span class="p">;</span></span>
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756
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<pre style="margin: 0;"> <span id="LC756" class="line" lang="objective_c"> <span class="k" style="font-weight: 600;">struct</span> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="686" style="width: 35px; color: rgba(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="775" style="width: 35px; color: rgba(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">@@ -686,10 +775,12 @@ class GffLoader {</td>
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686
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775
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<pre style="margin: 0;"> <span id="LC775" class="line" lang="objective_c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">dOvlSET</span><span class="o" style="font-weight: 600;">:</span><span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">//discard overlapping Single Exon Transcripts on any strand</span></span>
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687
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776
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<pre style="margin: 0;"> <span id="LC776" class="line" lang="objective_c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">forceExons</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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688
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777
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<pre style="margin: 0;"> <span id="LC777" class="line" lang="objective_c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">streamIn</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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778
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<pre style="margin: 0;">+<span id="LC778" class="line" lang="objective_c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">ensemblProc</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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779
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<pre style="margin: 0;">+<span id="LC779" class="line" lang="objective_c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">attrsFilter</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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689
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780
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<pre style="margin: 0;"> <span id="LC780" class="line" lang="objective_c"> <span class="p">};</span></span>
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<pre style="margin: 0;"> <span id="LC781" class="line" lang="objective_c"> <span class="p">};</span></span>
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782
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<pre style="margin: 0;"> <span id="LC782" class="line" lang="objective_c"></span>
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<pre style="margin: 0;">-<span id="LC692" class="line" lang="objective_c"> <span class="n" style="color: #333;">GffLoader</span><span class="p">()</span><span class="o" style="font-weight: 600;">:</span><span class="n" style="color: #333;">fname</span><span class="p">(),</span><span class="n" style="color: #333;">f</span><span class="p">(</span><span class="nb" style="color: #0086b3;">NULL</span><span class="p">),</span> <span class="n" style="color: #333;">names</span><span class="p">(</span><span class="nb" style="color: #0086b3;">NULL</span><span class="p">),</span> <span class="n" style="color: #333;">options</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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783
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<pre style="margin: 0;">+<span id="LC783" class="line" lang="objective_c"> <span class="n" style="color: #333;">GffLoader</span><span class="p">()</span><span class="o" style="font-weight: 600;">:</span><span class="n" style="color: #333;">fname</span><span class="p">(),</span><span class="n" style="color: #333;">f</span><span class="p">(</span><span class="nb" style="color: #0086b3;">NULL</span><span class="p">),</span> <span class="n" style="color: #333;">names</span><span class="p">(</span><span class="nb" style="color: #0086b3;">NULL</span><span class="p">),</span> <span class="n" style="color: #333;"><span class="idiff left">intronList</span></span><span class="p"><span class="idiff">(),</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">options</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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693
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<pre style="margin: 0;"> <span id="LC784" class="line" lang="objective_c"> <span class="n" style="color: #333;">transcriptsOnly</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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785
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<pre style="margin: 0;"> <span id="LC785" class="line" lang="objective_c"> <span class="n" style="color: #333;">gffnames_ref</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;">names</span><span class="p">);</span></span>
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695
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<pre style="margin: 0;"> <span id="LC786" class="line" lang="objective_c"> <span class="n" style="color: #333;">names</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">GffObj</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">names</span><span class="p">;</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -712,11 +803,15 @@ class GffLoader {</td>
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<pre style="margin: 0;"> <span id="LC803" class="line" lang="objective_c"> <span class="p">}</span></span>
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804
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<pre style="margin: 0;"> <span id="LC804" class="line" lang="objective_c"></span>
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<pre style="margin: 0;"> <span id="LC805" class="line" lang="objective_c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">validateGffRec</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>
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<pre style="margin: 0;">+<span id="LC806" class="line" lang="objective_c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">checkFilters</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>
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<pre style="margin: 0;">+<span id="LC807" class="line" lang="objective_c"></span>
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<pre style="margin: 0;">+<span id="LC808" class="line" lang="objective_c"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">collectIntrons</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;">t</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">//for -j output</span></span>
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809
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<pre style="margin: 0;"> <span id="LC809" class="line" lang="objective_c"></span>
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<pre style="margin: 0;"> <span id="LC810" class="line" lang="objective_c"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">load</span><span class="p">(</span><span class="n" style="color: #333;">GList</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">GenomicSeqData</span><span class="o" style="font-weight: 600;">>&</span><span class="n" style="color: #333;">seqdata</span><span class="p">,</span> <span class="n" style="color: #333;">GFFCommentParser</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">gf_parsecomment</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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811
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<pre style="margin: 0;"> <span id="LC811" class="line" lang="objective_c"></span>
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812
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<pre style="margin: 0;"> <span id="LC812" class="line" lang="objective_c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">placeGf</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;">t</span><span class="p">,</span> <span class="n" style="color: #333;">GenomicSeqData</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">gdata</span><span class="p">);</span></span>
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813
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<pre style="margin: 0;"> <span id="LC813" class="line" lang="objective_c"></span>
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<pre style="margin: 0;">+<span id="LC814" class="line" lang="objective_c"></span>
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<pre style="margin: 0;"> <span id="LC815" class="line" lang="objective_c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">unsplContained</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;">ti</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;">tj</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC816" class="line" lang="objective_c"> <span class="n" style="color: #333;">GffObj</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">redundantTranscripts</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;">ti</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;">tj</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC817" class="line" lang="objective_c"></span>
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<a href="https://salsa.debian.org/med-team/gffread/-/commit/8f84d6a4137aa1f105b971864eb5ea314c617754#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">@@ -4,24 +4,25 @@</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 "0.12.<span class="idiff left right">1</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 "0.12.<span class="idiff left right">4</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 <span class="idiff left right"><input_gff> [-g <genomic_seqs_fasta> | <dir>]</span>[-s <seq_info.fsize>] \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 <span class="idiff left right">[-g <genomic_seqs_fasta> | <dir>] </span>[-s <seq_info.fsize>] \n\</span></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"> [-o <outfile>] [-t <trackname>] [-r [[<strand>]<chr>:]<start>..<end> [-R]]\n\</span></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"> [-CTVNJMKQAFPGUBHZWTOLE] [-w <exons.fa>] [-x <cds.fa>] [-y <tr_cds.fa>]\n\</span></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"> [-i <maxintron>] [--stream] [--bed] [--table <attrlist>] [--sort-by <ref.lst>]\n\</span></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"> \n\</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"> [--ids <IDs.lst> | --nids <IDs.lst>] [--attrs <attr-list>] [-i <maxintron>]\n\</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"> [--stream] [--bed | --gtf | --tlf] [--table <attrlist>] [--sort-by <ref.lst>]\n\</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"> [<input_gff>] \n\n\</span></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"> Filter, convert or cluster GFF/GTF/BED records, extract the sequence of\n\</span></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"> transcripts (exon or CDS) and more.\n\</span></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"> By default (i.e. without -O) only transcripts are processed, discarding any\n\</span></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"> other non-transcript features. Default output is a simplified GFF3 with only\n\</span></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"> the basic attributes.\n\</span></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"> \n\</span></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"> <input_gff> is a GFF file, use '-' for stdin\n\</span></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"> \n\</span></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">Options:\n\</span></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"> -i discard transcripts having an intron larger than <maxintron>\n\</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"> --ids discard records/transcripts if their IDs are not listed in <IDs.lst>\n\</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"> --nids discard records/transcripts if their IDs are listed in <IDs.lst>\n\</span></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"> -l discard transcripts shorter than <minlen> bases\n\</span></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"> -r only show transcripts overlapping coordinate range <start>..<end>\n\</span></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"> (on chromosome/contig <chr>, strand <strand> if provided)\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">@@ -42,11 +43,13 @@ Sorting: (by default, chromosomes are kept in the order they were found)\n\</td>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"> --sort-by : sort the reference sequences by the order in which their\n\</span></span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"> names are given in the <refseq.lst> file\n\</span></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">Misc options: \n\</span></span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"> -F <span class="idiff left right">preserve</span> all GFF attributes (for non-exon features)\n\</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"> -F <span class="idiff left right">keep</span> all GFF attributes (for non-exon features)\n\</span></span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"> --keep-exon-attrs : for -F option, do not attempt to reduce redundant\n\</span></span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"> exon/CDS attributes\n\</span></span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"> -G do not keep exon attributes, move them to the transcript feature\n\</span></span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"> (for GFF3 output)\n\</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"> --attrs <attr-list> only output the GTF/GFF attributes listed in <attr-list>\n\</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"> which is a comma delimited list of attribute names to\n\</span></span>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"> --keep-genes : in transcript-only mode (default), also preserve gene records\n\</span></span>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"> --keep-comments: for GFF3 input/output, try to preserve comments\n\</span></span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"> -O process other non-transcript GFF records (by default non-transcript\n\</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -78,7 +81,7 @@ Misc options: \n\</td>
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"> ((no sorting, exons must be grouped by transcript in the input data)\n\</span></span>
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">Clustering:\n\</span></span>
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"> -M/--merge : cluster the input transcripts into loci, discarding\n\</span></span>
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<pre style="margin: 0;">-<span id="LC81" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"> \"<span class="idiff left right">duplicated</span>\" transcripts (those with the same exact introns\n\</span></span>
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<td class="diff-line-num new new_line" data-linenumber="84" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"> \"<span class="idiff left right">redundant</span>\" transcripts (those with the same exact introns\n\</span></span>
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"> and fully contained or equal boundaries)\n\</span></span>
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"> -d <dupinfo> : for -M option, write duplication info to file <dupinfo>\n\</span></span>
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<pre style="margin: 0;"> <span id="LC87" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"> --cluster-only: same as -M/--merge but without discarding any of the\n\</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -102,24 +105,26 @@ 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;"> -g full path to a multi-fasta file with the genomic sequences\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;"> for all input mappings, OR a directory with single-fasta files\n\</span></span>
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<td class="diff-line-num old_line" data-linenumber="104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC107" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"> (one per genomic sequence, with file names matching sequence names)\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;"> -j write a tab delimited file with all the junctions (intron coordinates)\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;"> -w write a fasta file with spliced exons for each transcript\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;"> --w-add <N> for the -w option, extract additional <N> bases\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;"> both upstream and downstream of the transcript boundaries\n\</span></span>
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<td class="diff-line-num new new_line" data-linenumber="112" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"> --w-nocds for -w, disable the output of CDS info in the FASTA file\n\</span></span>
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<td class="diff-line-num old_line" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC113" 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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<td class="diff-line-num old_line" data-linenumber="109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="114" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC114" 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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<td class="diff-line-num old_line" data-linenumber="110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
110
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<pre style="margin: 0;"> <span id="LC115" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"> -W for -w and -x options, write in the FASTA defline all the exon\n\</span></span>
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<td class="diff-line-num old_line" data-linenumber="111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="116" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC116" 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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<td class="diff-line-num new_line" data-linenumber="117" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC117" 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="LC113" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"> -L Ensembl GTF to GFF3 conversion<span class="idiff left right"> (implies -F; should be used with -m)</span>\n\</span></span>
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"> -L Ensembl GTF to GFF3 conversion<span class="idiff left right">, adds version to IDs</span>\n\</span></span>
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119
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<pre style="margin: 0;"> <span id="LC119" 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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115
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<pre style="margin: 0;"> <span id="LC120" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"> sequence names, having this 2-column format:\n\</span></span>
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116
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121
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<pre style="margin: 0;"> <span id="LC121" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"> <original_ref_ID> <new_ref_ID>\n\</span></span>
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117
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122
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<pre style="margin: 0;"> <span id="LC122" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"> -t use <trackname> in the 2nd column of each GFF/GTF output line\n\</span></span>
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118
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<pre style="margin: 0;">-<span id="LC118" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"> -o write the records into <outfile> instead of stdout\n\</span></span>
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"> -o write the <span class="idiff left right">output </span>records into <outfile> instead of stdout\n\</span></span>
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119
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<pre style="margin: 0;"> <span id="LC124" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"> -T main output will be GTF instead of GFF3\n\</span></span>
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<pre style="margin: 0;"> <span id="LC125" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"> --bed output records in BED format instead of default GFF3\n\</span></span>
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<pre style="margin: 0;"> <span id="LC126" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"> --tlf output \"transcript line format\" which is like GFF\n\</span></span>
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<pre style="margin: 0;">-<span id="LC122" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"> but <span class="idiff left right">exons, CDS features and related data are</span> stored as GFF \n\</span></span>
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"> but <span class="idiff left right">with exons and CDS related features</span> stored as GFF \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;"> attributes in the transcript feature line, like this:\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;"> exoncount=N;exons=<exons>;CDSphase=<N>;CDS=<CDScoords> \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;"> <exons> is a comma-delimited list of exon_start-exon_end coordinates;\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">@@ -136,61 +141,11 @@ Output options:\n\</td>
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<pre style="margin: 0;"> <span id="LC141" 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="LC142" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">"</span></span>
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<pre style="margin: 0;"> <span id="LC143" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC139" 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="LC140" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">FILE* ffasta=NULL;</span></span>
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<pre style="margin: 0;">-<span id="LC141" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">FILE* f_in=NULL;</span></span>
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<pre style="margin: 0;">-<span id="LC142" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">FILE* f_out=NULL;</span></span>
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<pre style="margin: 0;">-<span id="LC143" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">FILE* f_w=NULL; //writing fasta with spliced exons (transcripts)</span></span>
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<pre style="margin: 0;">-<span id="LC144" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">int wPadding = 0; //padding for -w option</span></span>
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<pre style="margin: 0;">-<span id="LC145" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">FILE* f_x=NULL; //writing fasta with spliced CDS</span></span>
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146
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<pre style="margin: 0;">-<span id="LC146" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">FILE* f_y=NULL; //wrting fasta with translated CDS</span></span>
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147
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<pre style="margin: 0;">-<span id="LC147" class="line" lang="cpp"></span>
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148
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<pre style="margin: 0;">-<span id="LC148" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">bool wCDSonly=false;</span></span>
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149
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<pre style="margin: 0;">-<span id="LC149" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">bool wNConly=false;</span></span>
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150
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<pre style="margin: 0;">-<span id="LC150" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">int minLen=0; //minimum transcript length</span></span>
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151
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<pre style="margin: 0;">-<span id="LC151" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">bool validCDSonly=false; // translation with no in-frame STOP</span></span>
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152
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<pre style="margin: 0;">-<span id="LC152" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">bool bothStrands=false; //for single-exon mRNA validation, check the other strand too</span></span>
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153
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<pre style="margin: 0;">-<span id="LC153" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">bool altPhases=false; //if original phase fails translation validation,</span></span>
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154
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<pre style="margin: 0;">-<span id="LC154" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> //try the other 2 phases until one makes it</span></span>
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155
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<pre style="margin: 0;">-<span id="LC155" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">bool addCDSattrs=false;</span></span>
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156
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<pre style="margin: 0;">-<span id="LC156" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">bool add_hasCDS=false;</span></span>
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157
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<pre style="margin: 0;">-<span id="LC157" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">//bool streamIn=false; // --stream option</span></span>
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158
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<pre style="margin: 0;">-<span id="LC158" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">bool adjustStop=false; //automatic adjust the CDS stop coordinate</span></span>
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159
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<pre style="margin: 0;">-<span id="LC159" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">bool covInfo=false; // --cov-info : only report genome coverage</span></span>
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160
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<pre style="margin: 0;">-<span id="LC160" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">GStr tableFormat; //list of "attributes" to print in tab delimited format</span></span>
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161
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<pre style="margin: 0;">-<span id="LC161" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">bool spliceCheck=false; //only known splice-sites</span></span>
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162
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<pre style="margin: 0;">-<span id="LC162" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">bool decodeChars=false; //decode url-encoded chars in attrs (-D)</span></span>
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163
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<pre style="margin: 0;">-<span id="LC163" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">bool StarStop=false; //use * instead of . for stop codon translation</span></span>
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164
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<pre style="margin: 0;">-<span id="LC164" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">bool fullCDSonly=false; // starts with START, ends with STOP codon</span></span>
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165
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<pre style="margin: 0;">-<span id="LC165" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">*/</span></span>
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166
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<pre style="margin: 0;">-<span id="LC166" class="line" lang="cpp"></span>
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167
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144
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<pre style="margin: 0;"> <span id="LC144" class="line" lang="cpp"><span class="n" style="color: #333;">GStr</span> <span class="n" style="color: #333;">sortBy</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">//file name with chromosomes listed in the desired order</span></span>
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168
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<pre style="margin: 0;"> <span id="LC145" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC146" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">BEDinput</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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170
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147
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<pre style="margin: 0;"> <span id="LC147" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">TLFinput</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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171
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148
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<pre style="margin: 0;"> <span id="LC148" class="line" lang="cpp"></span>
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172
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<pre style="margin: 0;">-<span id="LC172" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//--- output options</span></span>
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173
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<pre style="margin: 0;">-<span id="LC173" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/*</span></span>
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174
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<pre style="margin: 0;">-<span id="LC174" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">extern bool fmtGFF3=true; //default output: GFF3</span></span>
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175
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<pre style="margin: 0;">-<span id="LC175" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">//other formats only make sense in transcriptOnly mode</span></span>
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176
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<pre style="margin: 0;">-<span id="LC176" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">extern bool fmtGTF=false;</span></span>
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177
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<pre style="margin: 0;">-<span id="LC177" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">extern bool fmtBED=false;</span></span>
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178
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<pre style="margin: 0;">-<span id="LC178" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">extern bool fmtTLF=false;</span></span>
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179
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<pre style="margin: 0;">-<span id="LC179" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">extern bool fmtTable=false;</span></span>
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180
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<pre style="margin: 0;">-<span id="LC180" class="line" lang="cpp"></span>
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181
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<pre style="margin: 0;">-<span id="LC181" class="line" lang="cpp"></span>
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182
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<pre style="margin: 0;">-<span id="LC182" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">bool multiExon=false;</span></span>
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183
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<pre style="margin: 0;">-<span id="LC183" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">bool writeExonSegs=false;</span></span>
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184
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<pre style="margin: 0;">-<span id="LC184" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">char* tracklabel=NULL;</span></span>
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185
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<pre style="margin: 0;">-<span id="LC185" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">char* rfltGSeq=NULL;</span></span>
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186
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<pre style="margin: 0;">-<span id="LC186" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">char rfltStrand=0;</span></span>
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187
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<pre style="margin: 0;">-<span id="LC187" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">uint rfltStart=0;</span></span>
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188
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<pre style="margin: 0;">-<span id="LC188" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">uint rfltEnd=MAX_UINT;</span></span>
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189
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<pre style="margin: 0;">-<span id="LC189" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">bool rfltWithin=false; //check for full containment within given range</span></span>
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190
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<pre style="margin: 0;">-<span id="LC190" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">bool addDescr=false;</span></span>
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191
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<pre style="margin: 0;">-<span id="LC191" class="line" lang="cpp"></span>
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192
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<pre style="margin: 0;">-<span id="LC192" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">*/</span></span>
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193
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<pre style="margin: 0;">-<span id="LC193" class="line" lang="cpp"></span>
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149
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<pre style="margin: 0;"> <span id="LC149" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//bool protmap=false;</span></span>
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195
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150
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<pre style="margin: 0;"> <span id="LC150" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//int maxintron=999000000;</span></span>
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196
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151
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<pre style="margin: 0;"> <span id="LC151" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//bool mergeCloseExons=false;</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">@@ -200,7 +155,22 @@ GffLoader gffloader;</td>
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200
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155
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<pre style="margin: 0;"> <span id="LC155" class="line" lang="cpp"></span>
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201
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156
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<pre style="margin: 0;"> <span id="LC156" class="line" lang="cpp"><span class="n" style="color: #333;">GList</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">GenomicSeqData</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">g_data</span><span class="p">(</span><span class="nb" style="color: #0086b3;">true</span><span class="p">,</span><span class="nb" style="color: #0086b3;">true</span><span class="p">,</span><span class="nb" style="color: #0086b3;">true</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">//list of GFF records by genomic seq</span></span>
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202
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157
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<pre style="margin: 0;"> <span id="LC157" class="line" lang="cpp"></span>
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203
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<pre style="margin: 0;">-<span id="LC203" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">loadSeqInfo</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;">GHash</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">SeqInfo</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">si</span><span class="p">)</span> <span class="p">{</span></span>
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158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">loadIDlist</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;">GStrSet</span><span class="o" style="font-weight: 600;"><></span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">idhash</span><span class="p">)</span> <span class="p">{</span></span>
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159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="cpp"> <span class="n" style="color: #333;">GLineReader</span> <span class="n" style="color: #333;">fr</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">);</span></span>
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160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">fr</span><span class="p">.</span><span class="n" style="color: #333;">isEof</span><span class="p">())</span> <span class="p">{</span></span>
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161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="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;">line</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">fr</span><span class="p">.</span><span class="n" style="color: #333;">getLine</span><span class="p">();</span></span>
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162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">line</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;">break</span><span class="p">;</span></span>
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163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">line</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="k" style="font-weight: 600;">continue</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">//skip comments</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;">GDynArray</span><span class="o" style="font-weight: 600;"><</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;">ids</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="165" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="cpp"> <span class="n" style="color: #333;">strsplit</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">,</span> <span class="n" style="color: #333;">ids</span><span class="p">);</span></span>
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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">uint</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;">ids</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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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">strlen</span><span class="p">(</span><span class="n" style="color: #333;">ids</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">])</span><span class="o" style="font-weight: 600;">></span><span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="cpp"> <span class="n" style="color: #333;">idhash</span><span class="p">.</span><span class="n" style="color: #333;">Add</span><span class="p">(</span><span class="n" style="color: #333;">ids</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]);</span></span>
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">loadSeqInfo</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;">GHash</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">SeqInfo</span><span class="o" style="font-weight: 600;">*></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">si</span><span class="p">)</span> <span class="p">{</span></span>
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204
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174
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<pre style="margin: 0;"> <span id="LC174" class="line" lang="cpp"> <span class="n" style="color: #333;">GLineReader</span> <span class="n" style="color: #333;">fr</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">);</span></span>
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205
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175
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<pre style="margin: 0;"> <span id="LC175" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">fr</span><span class="p">.</span><span class="n" style="color: #333;">isEof</span><span class="p">())</span> <span class="p">{</span></span>
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206
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176
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<pre style="margin: 0;"> <span id="LC176" 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;">line</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">fr</span><span class="p">.</span><span class="n" style="color: #333;">getLine</span><span class="p">();</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="230" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="200" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -230,23 +200,33 @@ void loadSeqInfo(FILE* f, GHash<SeqInfo> &si) {</td>
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230
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200
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<pre style="margin: 0;"> <span id="LC200" class="line" lang="cpp"> <span class="p">}</span> <span class="c1" style="color: #998; font-style: italic;">//while lines</span></span>
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201
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<pre style="margin: 0;"> <span id="LC201" class="line" lang="cpp"><span class="p">}</span></span>
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202
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<pre style="margin: 0;"> <span id="LC202" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">getAttrList</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;">s</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC204" 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="n" style="color: #333;">is_empty</span><span class="p">())</span> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>
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205
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="cpp"> <span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">startTokenize</span><span class="p">(</span><span class="s" style="color: #d14;">",;:"</span><span class="p">,</span> <span class="n" style="color: #333;">tkCharSet</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="cpp"> <span class="n" style="color: #333;">GStr</span> <span class="n" style="color: #333;">w</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC207" 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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<pre style="margin: 0;">+<span id="LC208" 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="n" style="color: #333;">length</span><span class="p">()</span><span class="o" style="font-weight: 600;">></span><span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="cpp"> <span class="n" style="color: #333;">attrList</span><span class="p">.</span><span class="n" style="color: #333;">Add</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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<pre style="margin: 0;">+<span id="LC210" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC213" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">setTableFormat</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;">s</span><span class="p">)</span> <span class="p">{</span></span>
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234
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<td class="diff-line-num new_line" data-linenumber="214" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
214
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<pre style="margin: 0;"> <span id="LC214" 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="n" style="color: #333;">is_empty</span><span class="p">())</span> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="235" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
235
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<td class="diff-line-num new_line" data-linenumber="215" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
215
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<pre style="margin: 0;"> <span id="LC215" class="line" lang="cpp"> <span class="n" style="color: #333;">GHash</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">ETableFieldType</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">specialFields</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="236" 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">
236
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<td class="diff-line-num new_line old" data-linenumber="216" 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="LC236" 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;"><span class="idiff left">new</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">ETableFieldType</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">ctfGFF_chr</span></span><span class="p"><span class="idiff right">)</span>);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="237" 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">
237
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<td class="diff-line-num new_line old" data-linenumber="216" 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="LC237" 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;"><span class="idiff left">new</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">ETableFieldType</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">ctfGFF_ID</span></span><span class="p"><span class="idiff right">)</span>);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="238" 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">
238
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<td class="diff-line-num new_line old" data-linenumber="216" 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="LC238" 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;"><span class="idiff left">new</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">ETableFieldType</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">ctfGFF_geneID</span></span><span class="p"><span class="idiff right">)</span>);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="239" 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">
239
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<td class="diff-line-num new_line old" data-linenumber="216" 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="LC239" 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;"><span class="idiff left">new</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">ETableFieldType</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">ctfGFF_geneName</span></span><span class="p"><span class="idiff right">)</span>);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="240" 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">
240
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<td class="diff-line-num new_line old" data-linenumber="216" 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="LC240" 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;"><span class="idiff left">new</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">ETableFieldType</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">ctfGFF_Parent</span></span><span class="p"><span class="idiff right">)</span>);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="241" 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">
241
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<td class="diff-line-num new_line old" data-linenumber="216" 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="LC241" 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;"><span class="idiff left">new</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">ETableFieldType</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">ctfGFF_feature</span></span><span class="p"><span class="idiff right">)</span>);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="242" 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">
242
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<td class="diff-line-num new_line old" data-linenumber="216" 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="LC242" 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;"><span class="idiff left">new</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">ETableFieldType</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">ctfGFF_start</span></span><span class="p"><span class="idiff right">)</span>);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="243" 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">
243
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<td class="diff-line-num new_line old" data-linenumber="216" 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="LC243" 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;">"end"</span><span class="p">,</span> <span class="k" style="font-weight: 600;"><span class="idiff left">new</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">ETableFieldType</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">ctfGFF_end</span></span><span class="p"><span class="idiff right">)</span>);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="244" 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">
244
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<td class="diff-line-num new_line old" data-linenumber="216" 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="LC244" 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;">"strand"</span><span class="p">,</span> <span class="k" style="font-weight: 600;"><span class="idiff left">new</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">ETableFieldType</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">ctfGFF_strand</span></span><span class="p"><span class="idiff right">)</span>);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="245" 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">
245
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<td class="diff-line-num new_line old" data-linenumber="216" 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="LC245" 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;">"numexons"</span><span class="p">,</span> <span class="k" style="font-weight: 600;"><span class="idiff left">new</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">ETableFieldType</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">ctfGFF_numexons</span></span><span class="p"><span class="idiff right">)</span>);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="246" 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">
246
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<td class="diff-line-num new_line old" data-linenumber="216" 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="LC246" 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;">"exons"</span><span class="p">,</span> <span class="k" style="font-weight: 600;"><span class="idiff left">new</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">ETableFieldType</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">ctfGFF_exons</span></span><span class="p"><span class="idiff right">)</span>);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="247" 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">
247
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<td class="diff-line-num new_line old" data-linenumber="216" 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="LC247" 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;">"cds"</span><span class="p">,</span> <span class="k" style="font-weight: 600;"><span class="idiff left">new</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">ETableFieldType</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">ctfGFF_cds</span></span><span class="p"><span class="idiff right">)</span>);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="248" 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">
248
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<td class="diff-line-num new_line old" data-linenumber="216" 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="LC248" 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;">"covlen"</span><span class="p">,</span> <span class="k" style="font-weight: 600;"><span class="idiff left">new</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">ETableFieldType</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">ctfGFF_covlen</span></span><span class="p"><span class="idiff right">)</span>);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="249" 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">
249
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<td class="diff-line-num new_line old" data-linenumber="216" 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="LC249" 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;">"cdslen"</span><span class="p">,</span> <span class="k" style="font-weight: 600;"><span class="idiff left">new</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">ETableFieldType</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">ctfGFF_cdslen</span></span><span class="p"><span class="idiff right">)</span>);</span></span>
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<td class="diff-line-num new old_line" data-linenumber="250" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="216" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
216
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<pre style="margin: 0;">+<span id="LC216" 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="n" style="color: #333;"><span class="idiff left right">ctfGFF_chr</span></span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="217" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
217
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<pre style="margin: 0;">+<span id="LC217" 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="n" style="color: #333;"><span class="idiff left right">ctfGFF_ID</span></span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="218" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
218
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<pre style="margin: 0;">+<span id="LC218" 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="n" style="color: #333;"><span class="idiff left right">ctfGFF_geneID</span></span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="219" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
219
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<pre style="margin: 0;">+<span id="LC219" 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="n" style="color: #333;"><span class="idiff left right">ctfGFF_geneName</span></span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="220" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
220
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<pre style="margin: 0;">+<span id="LC220" 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="n" style="color: #333;"><span class="idiff left right">ctfGFF_Parent</span></span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="221" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
221
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<pre style="margin: 0;">+<span id="LC221" 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="n" style="color: #333;"><span class="idiff left right">ctfGFF_feature</span></span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="222" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
222
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<pre style="margin: 0;">+<span id="LC222" 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="n" style="color: #333;"><span class="idiff left right">ctfGFF_start</span></span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="223" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
223
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<pre style="margin: 0;">+<span id="LC223" 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;">"end"</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">ctfGFF_end</span></span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="224" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
224
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<pre style="margin: 0;">+<span id="LC224" 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;">"strand"</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">ctfGFF_strand</span></span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="225" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
225
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<pre style="margin: 0;">+<span id="LC225" 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;">"numexons"</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">ctfGFF_numexons</span></span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="226" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
226
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<pre style="margin: 0;">+<span id="LC226" 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;">"exons"</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">ctfGFF_exons</span></span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="227" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
227
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<pre style="margin: 0;">+<span id="LC227" 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;">"cds"</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">ctfGFF_cds</span></span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="228" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
228
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<pre style="margin: 0;">+<span id="LC228" 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;">"covlen"</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">ctfGFF_covlen</span></span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="229" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
229
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<pre style="margin: 0;">+<span id="LC229" 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;">"cdslen"</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">ctfGFF_cdslen</span></span><span class="p">);</span></span>
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250
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230
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<pre style="margin: 0;"> <span id="LC230" class="line" lang="cpp"></span>
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251
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231
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<pre style="margin: 0;"> <span id="LC231" class="line" lang="cpp"> <span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">startTokenize</span><span class="p">(</span><span class="s" style="color: #d14;">" ,;.:"</span><span class="p">,</span> <span class="n" style="color: #333;">tkCharSet</span><span class="p">);</span></span>
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252
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232
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<pre style="margin: 0;"> <span id="LC232" class="line" lang="cpp"> <span class="n" style="color: #333;">GStr</span> <span class="n" style="color: #333;">w</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="287" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="267" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -287,7 +267,7 @@ void setTableFormat(GStr& s) {</td>
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287
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267
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<pre style="margin: 0;"> <span id="LC267" class="line" lang="cpp"> <span class="p">}</span></span>
</pre>
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288
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268
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<pre style="margin: 0;"> <span id="LC268" class="line" lang="cpp"><span class="p">}</span></span>
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289
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269
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<pre style="margin: 0;"> <span id="LC269" class="line" lang="cpp"></span>
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290
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<pre style="margin: 0;">-<span id="LC290" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">loadRefTable</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;">GHash</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">RefTran</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">rt</span><span class="p">)</span> <span class="p">{</span></span>
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270
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<pre style="margin: 0;">+<span id="LC270" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">loadRefTable</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;">GHash</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">RefTran</span><span class="o" style="font-weight: 600;"><span class="idiff left right">*</span>>&</span> <span class="n" style="color: #333;">rt</span><span class="p">)</span> <span class="p">{</span></span>
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291
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271
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<pre style="margin: 0;"> <span id="LC271" class="line" lang="cpp"> <span class="n" style="color: #333;">GLineReader</span> <span class="n" style="color: #333;">fr</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">);</span></span>
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292
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272
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<pre style="margin: 0;"> <span id="LC272" 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;">line</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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293
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273
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<pre style="margin: 0;"> <span id="LC273" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span> <span class="p">((</span><span class="n" style="color: #333;">line</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">fr</span><span class="p">.</span><span class="n" style="color: #333;">getLine</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="417" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="397" style="width: 35px; color: rgba(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">@@ -417,15 +397,17 @@ void shutDown() {</td>
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417
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397
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<pre style="margin: 0;"> <span id="LC397" class="line" lang="cpp"> <span class="n" style="color: #333;">FWCLOSE</span><span class="p">(</span><span class="n" style="color: #333;">f_w</span><span class="p">);</span></span>
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418
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398
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<pre style="margin: 0;"> <span id="LC398" class="line" lang="cpp"> <span class="n" style="color: #333;">FWCLOSE</span><span class="p">(</span><span class="n" style="color: #333;">f_x</span><span class="p">);</span></span>
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419
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399
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<pre style="margin: 0;"> <span id="LC399" class="line" lang="cpp"> <span class="n" style="color: #333;">FWCLOSE</span><span class="p">(</span><span class="n" style="color: #333;">f_y</span><span class="p">);</span></span>
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400
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<pre style="margin: 0;">+<span id="LC400" class="line" lang="cpp"> <span class="n" style="color: #333;">FWCLOSE</span><span class="p">(</span><span class="n" style="color: #333;">f_j</span><span class="p">);</span></span>
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401
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<pre style="margin: 0;"> <span id="LC401" class="line" lang="cpp"><span class="p">}</span></span>
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402
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<pre style="margin: 0;"> <span id="LC402" class="line" lang="cpp"></span>
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422
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403
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<pre style="margin: 0;"> <span id="LC403" 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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404
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<pre style="margin: 0;"> <span id="LC404" class="line" lang="cpp"> <span class="n" style="color: #333;">GArgs</span> <span class="n" style="color: #333;">args</span><span class="p">(</span><span class="n" style="color: #333;">argc</span><span class="p">,</span> <span class="n" style="color: #333;">argv</span><span class="p">,</span></span>
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405
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<pre style="margin: 0;"> <span id="LC405" class="line" lang="cpp"> <span class="s" style="color: #d14;">"version;debug;merge;stream;adj-stop;bed;in-bed;tlf;in-tlf;cluster-only;nc;cov-info;help;"</span></span>
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<pre style="margin: 0;">-<span id="LC425" class="line" lang="cpp"> <span class="s" style="color: #d14;">"sort-alpha;keep-genes;w-<span class="idiff left right">add=</span>;keep-comments;keep-exon-attrs;force-exons;t-adopt;gene2exon;"</span></span>
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<pre style="margin: 0;">-<span id="LC426" class="line" lang="cpp"> <span class="s" style="color: #d14;">"ignore-locus;no-pseudo;table=sort-by=hvOUNHPWCVJMKQYTDARSZFGLEBm:g:i:r:s:l:t:o:w:x:y:d:"</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC406" class="line" lang="cpp"> <span class="s" style="color: #d14;">"sort-alpha;keep-genes;w-<span class="idiff left right">nocds;attrs=;w-add=;ids=;nids=0;gtf</span>;keep-comments;keep-exon-attrs;force-exons;t-adopt;gene2exon;"</span></span>
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<pre style="margin: 0;">+<span id="LC407" class="line" lang="cpp"> <span class="s" style="color: #d14;">"ignore-locus;no-pseudo;table=sort-by=hvOUNHPWCVJMKQYTDARSZFGLEBm:g:i:r:s:l:t:o:w:x:y:<span class="idiff left right">j:</span>d:"</span><span class="p">);</span></span>
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408
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<pre style="margin: 0;"> <span id="LC408" class="line" lang="cpp"> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">printError</span><span class="p">(</span><span class="n" style="color: #333;">USAGE</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="LC428" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">getOpt</span><span class="p">(</span><span class="sc" style="color: #d14;">'h'</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">getOpt</span><span class="p">(</span><span class="s" style="color: #d14;">"help"</span><span class="p">))</span> <span class="p">{</span></span>
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409
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<pre style="margin: 0;">+<span id="LC409" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">numfiles</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">startNonOpt</span><span class="p">();</span></span>
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410
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<pre style="margin: 0;">+<span id="LC410" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">getOpt</span><span class="p">(</span><span class="sc" style="color: #d14;">'h'</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">getOpt</span><span class="p">(</span><span class="s" style="color: #d14;">"help"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span> <span class="n" style="color: #333;">numfiles</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">hasStdInput</span><span class="p">()))</span> <span class="p">{</span></span>
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429
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411
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<pre style="margin: 0;"> <span id="LC411" class="line" lang="cpp"> <span class="n" style="color: #333;">GMessage</span><span class="p">(</span><span class="s" style="color: #d14;">"%s"</span><span class="p">,</span><span class="n" style="color: #333;">USAGE</span><span class="p">);</span></span>
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430
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412
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<pre style="margin: 0;"> <span id="LC412" class="line" lang="cpp"> <span class="n" style="color: #333;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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431
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413
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<pre style="margin: 0;"> <span id="LC413" 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="448" style="width: 35px; color: rgba(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="430" style="width: 35px; color: rgba(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">@@ -448,9 +430,9 @@ int main(int argc, char* argv[]) {</td>
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448
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430
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<pre style="margin: 0;"> <span id="LC430" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">adjustStop</span><span class="p">)</span> <span class="n" style="color: #333;">addCDSattrs</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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449
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431
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<pre style="margin: 0;"> <span id="LC431" class="line" lang="cpp"> <span class="n" style="color: #333;">validCDSonly</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">getOpt</span><span class="p">(</span><span class="sc" style="color: #d14;">'V'</span><span class="p">)</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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450
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432
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<pre style="margin: 0;"> <span id="LC432" class="line" lang="cpp"> <span class="n" style="color: #333;">altPhases</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">getOpt</span><span class="p">(</span><span class="sc" style="color: #d14;">'H'</span><span class="p">)</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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451
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<pre style="margin: 0;">-<span id="LC451" class="line" lang="cpp"> <span class="n" style="color: #333;">fmtGTF</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">getOpt</span><span class="p">(</span><span class="sc" style="color: #d14;">'T'</span><span class="p">)</span><span class="o" style="font-weight: 600;">!=</span><span class="nb" style="color: #0086b3;">NULL</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">//switch output format to GTF</span></span>
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<td class="diff-line-num old old_line" data-linenumber="452" 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">
452
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<pre style="margin: 0;">-<span id="LC452" class="line" lang="cpp"> <span class="n" style="color: #333;">fmtBED</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">getOpt</span><span class="p">(</span><span class="s" style="color: #d14;">"bed"</span><span class="p">)</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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453
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<pre style="margin: 0;">-<span id="LC453" class="line" lang="cpp"> <span class="n" style="color: #333;">fmtTLF</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">getOpt</span><span class="p">(</span><span class="s" style="color: #d14;">"tlf"</span><span class="p">)</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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433
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<pre style="margin: 0;">+<span id="LC433" class="line" lang="cpp"> <span class="n" style="color: #333;">fmtGTF</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">getOpt</span><span class="p">(</span><span class="sc" style="color: #d14;">'T'</span><span class="p">)</span><span class="o" style="font-weight: 600;">!=</span><span class="nb" style="color: #0086b3;">NULL</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">||</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">args</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">getOpt</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"gtf"</span></span><span class="p"><span class="idiff">)</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 class="c1" style="color: #998; font-style: italic;">//switch output format to GTF</span></span>
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434
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<pre style="margin: 0;">+<span id="LC434" class="line" lang="cpp"> <span class="n" style="color: #333;">fmtBED</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">getOpt</span><span class="p">(</span><span class="s" style="color: #d14;">"bed"</span><span class="p">)</span><span class="o" style="font-weight: 600;">!=</span><span class="nb" style="color: #0086b3;">NULL</span><span class="p">);</span><span class="idiff left"> </span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right">//BED output</span></span></span>
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<td class="diff-line-num new new_line" data-linenumber="435" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
435
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<pre style="margin: 0;">+<span id="LC435" class="line" lang="cpp"> <span class="n" style="color: #333;">fmtTLF</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">getOpt</span><span class="p">(</span><span class="s" style="color: #d14;">"tlf"</span><span class="p">)</span><span class="o" style="font-weight: 600;">!=</span><span class="nb" style="color: #0086b3;">NULL</span><span class="p">);</span><span class="idiff left"> </span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right">//TLF output</span></span></span>
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454
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436
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<pre style="margin: 0;"> <span id="LC436" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">fmtGTF</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">fmtBED</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">fmtTLF</span><span class="p">)</span> <span class="p">{</span></span>
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455
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437
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<pre style="margin: 0;"> <span id="LC437" 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;">gffloader</span><span class="p">.</span><span class="n" style="color: #333;">transcriptsOnly</span><span class="p">)</span> <span class="p">{</span></span>
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456
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438
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<pre style="margin: 0;"> <span id="LC438" class="line" lang="cpp"> <span class="n" style="color: #333;">GMessage</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: option -O is only supported with GFF3 output"</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="510" style="width: 35px; color: rgba(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="492" style="width: 35px; color: rgba(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">@@ -510,7 +492,7 @@ int main(int argc, char* argv[]) {</td>
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510
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492
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<pre style="margin: 0;"> <span id="LC492" class="line" lang="cpp"> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">printCmdLine</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">);</span></span>
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511
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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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512
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494
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<pre style="margin: 0;"> <span id="LC494" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">getOpt</span><span class="p">(</span><span class="s" style="color: #d14;">"version"</span><span class="p">))</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;"><span class="idiff left right">GMessage</span></span><span class="p">(</span><span class="n" style="color: #333;">VERSION</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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495
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<pre style="margin: 0;">+<span id="LC495" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left right">printf</span></span><span class="p">(</span><span class="n" style="color: #333;">VERSION</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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514
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496
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<pre style="margin: 0;"> <span id="LC496" class="line" lang="cpp"> <span class="n" style="color: #333;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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515
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497
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<pre style="margin: 0;"> <span id="LC497" class="line" lang="cpp"> <span class="p">}</span></span>
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516
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498
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<pre style="margin: 0;"> <span id="LC498" class="line" lang="cpp"> <span class="n" style="color: #333;">gffloader</span><span class="p">.</span><span class="n" style="color: #333;">fullAttributes</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">getOpt</span><span class="p">(</span><span class="sc" style="color: #d14;">'F'</span><span class="p">)</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 unfold js-unfold old_line" data-linenumber="529" style="width: 35px; color: rgba(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="511" style="width: 35px; color: rgba(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">@@ -529,8 +511,8 @@ int main(int argc, char* argv[]) {</td>
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529
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511
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<pre style="margin: 0;"> <span id="LC511" class="line" lang="cpp"> <span class="n" style="color: #333;">gffloader</span><span class="p">.</span><span class="n" style="color: #333;">gatherExonAttrs</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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530
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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;">gffloader</span><span class="p">.</span><span class="n" style="color: #333;">fullAttributes</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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531
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513
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<pre style="margin: 0;"> <span id="LC513" class="line" lang="cpp"> <span class="p">}</span></span>
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532
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<pre style="margin: 0;">-<span id="LC532" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left right">ensembl_convert</span></span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">getOpt</span><span class="p">(</span><span class="sc" style="color: #d14;">'L'</span><span class="p">)</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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533
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<pre style="margin: 0;">-<span id="LC533" 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 right">ensembl_convert</span></span><span class="p">)</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="n" style="color: #333;"><span class="idiff left">gffloader</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">ensemblProc</span></span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">getOpt</span><span class="p">(</span><span class="sc" style="color: #d14;">'L'</span><span class="p">)</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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515
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<pre style="margin: 0;">+<span id="LC515" 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">gffloader</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">ensemblProc</span></span><span class="p">)</span> <span class="p">{</span></span>
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534
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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;">gffloader</span><span class="p">.</span><span class="n" style="color: #333;">fullAttributes</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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535
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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;">gffloader</span><span class="p">.</span><span class="n" style="color: #333;">gatherExonAttrs</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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536
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518
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<pre style="margin: 0;"> <span id="LC518" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//sortByLoc=true;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="558" style="width: 35px; color: rgba(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="540" style="width: 35px; color: rgba(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">@@ -558,7 +540,7 @@ int main(int argc, char* argv[]) {</td>
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558
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540
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<pre style="margin: 0;"> <span id="LC540" 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;">s</span><span class="p">.</span><span class="n" style="color: #333;">is_empty</span><span class="p">())</span> <span class="n" style="color: #333;">maxintron</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">asInt</span><span class="p">();</span></span>
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559
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541
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<pre style="margin: 0;"> <span id="LC541" class="line" lang="cpp"> <span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">getOpt</span><span class="p">(</span><span class="sc" style="color: #d14;">'l'</span><span class="p">);</span></span>
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560
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542
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<pre style="margin: 0;"> <span id="LC542" 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;">s</span><span class="p">.</span><span class="n" style="color: #333;">is_empty</span><span class="p">())</span> <span class="n" style="color: #333;">minLen</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">asInt</span><span class="p">();</span></span>
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561
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<pre style="margin: 0;">-<span id="LC561" class="line" lang="cpp"></span>
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543
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<pre style="margin: 0;">+<span id="LC543" class="line" lang="cpp"> <span class="n" style="color: #333;">TFilters</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="n" style="color: #333;">multiExon</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">wCDSonly</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">wNConly</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">//TODO: all transcript filters should be included here through validateGffRec()</span></span>
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562
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544
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<pre style="margin: 0;"> <span id="LC544" class="line" lang="cpp"> <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_repl</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">//duplicate/collapsing info output file</span></span>
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563
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545
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<pre style="margin: 0;"> <span id="LC545" class="line" lang="cpp"> <span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">getOpt</span><span class="p">(</span><span class="sc" style="color: #d14;">'d'</span><span class="p">);</span></span>
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564
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546
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<pre style="margin: 0;"> <span id="LC546" 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;">s</span><span class="p">.</span><span class="n" style="color: #333;">is_empty</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="569" style="width: 35px; color: rgba(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="551" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -569,6 +551,12 @@ int main(int argc, char* argv[]) {</td>
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569
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551
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<pre style="margin: 0;"> <span id="LC551" class="line" lang="cpp"> <span class="p">}</span></span>
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570
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552
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<pre style="margin: 0;"> <span id="LC552" class="line" lang="cpp"> <span class="p">}</span></span>
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571
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553
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<pre style="margin: 0;"> <span id="LC553" class="line" lang="cpp"></span>
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554
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<pre style="margin: 0;">+<span id="LC554" class="line" lang="cpp"> <span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">getOpt</span><span class="p">(</span><span class="s" style="color: #d14;">"attrs"</span><span class="p">);</span></span>
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555
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<pre style="margin: 0;">+<span id="LC555" 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;">s</span><span class="p">.</span><span class="n" style="color: #333;">is_empty</span><span class="p">())</span> <span class="p">{</span></span>
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556
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<pre style="margin: 0;">+<span id="LC556" class="line" lang="cpp"> <span class="n" style="color: #333;">getAttrList</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">);</span></span>
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557
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<pre style="margin: 0;">+<span id="LC557" class="line" lang="cpp"> <span class="n" style="color: #333;">gffloader</span><span class="p">.</span><span class="n" style="color: #333;">attrsFilter</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="n" style="color: #333;">attrList</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;">1</span><span class="p">);</span></span>
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558
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<pre style="margin: 0;">+<span id="LC558" class="line" lang="cpp"> <span class="n" style="color: #333;">gffloader</span><span class="p">.</span><span class="n" style="color: #333;">fullAttributes</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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559
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<pre style="margin: 0;">+<span id="LC559" class="line" lang="cpp"> <span class="p">}</span></span>
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572
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560
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<pre style="margin: 0;"> <span id="LC560" class="line" lang="cpp"> <span class="n" style="color: #333;">rfltWithin</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">getOpt</span><span class="p">(</span><span class="sc" style="color: #d14;">'R'</span><span class="p">)</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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573
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561
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<pre style="margin: 0;"> <span id="LC561" class="line" lang="cpp"> <span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">getOpt</span><span class="p">(</span><span class="sc" style="color: #d14;">'r'</span><span class="p">);</span></span>
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574
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562
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<pre style="margin: 0;"> <span id="LC562" 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;">s</span><span class="p">.</span><span class="n" style="color: #333;">is_empty</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="621" style="width: 35px; color: rgba(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="609" style="width: 35px; color: rgba(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">@@ -621,8 +609,25 @@ int main(int argc, char* argv[]) {</td>
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621
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609
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<pre style="margin: 0;"> <span id="LC609" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">fsize</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;">GError</span><span class="p">(</span><span class="s" style="color: #d14;">"Error opening info file: %s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">chars</span><span class="p">());</span></span>
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622
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610
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<pre style="margin: 0;"> <span id="LC610" class="line" lang="cpp"> <span class="n" style="color: #333;">loadSeqInfo</span><span class="p">(</span><span class="n" style="color: #333;">fsize</span><span class="p">,</span> <span class="n" style="color: #333;">seqinfo</span><span class="p">);</span></span>
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623
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611
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<pre style="margin: 0;"> <span id="LC611" class="line" lang="cpp"> <span class="n" style="color: #333;">fclose</span><span class="p">(</span><span class="n" style="color: #333;">fsize</span><span class="p">);</span></span>
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612
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<pre style="margin: 0;">+<span id="LC612" class="line" lang="cpp"> <span class="p">}</span></span>
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613
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<pre style="margin: 0;">+<span id="LC613" class="line" lang="cpp"> <span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">getOpt</span><span class="p">(</span><span class="s" style="color: #d14;">"ids"</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="614" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
614
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<pre style="margin: 0;">+<span id="LC614" 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="n" style="color: #333;">is_empty</span><span class="p">())</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="615" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
615
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<pre style="margin: 0;">+<span id="LC615" class="line" lang="cpp"> <span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">getOpt</span><span class="p">(</span><span class="s" style="color: #d14;">"nids"</span><span class="p">);</span></span>
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616
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<pre style="margin: 0;">+<span id="LC616" 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;">s</span><span class="p">.</span><span class="n" style="color: #333;">is_empty</span><span class="p">())</span></span>
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<td class="diff-line-num new new_line" data-linenumber="617" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
617
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<pre style="margin: 0;">+<span id="LC617" class="line" lang="cpp"> <span class="n" style="color: #333;">IDflt</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">idFlt_Exclude</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="618" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
618
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<pre style="margin: 0;">+<span id="LC618" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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619
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<pre style="margin: 0;">+<span id="LC619" class="line" lang="cpp"> <span class="n" style="color: #333;">IDflt</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">idFlt_Only</span><span class="p">;</span></span>
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620
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<pre style="margin: 0;">+<span id="LC620" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="621" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
621
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<pre style="margin: 0;">+<span id="LC621" 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;">s</span><span class="p">.</span><span class="n" style="color: #333;">is_empty</span><span class="p">())</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="622" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
622
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<pre style="margin: 0;">+<span id="LC622" class="line" lang="cpp"> <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="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">fopen</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">,</span><span class="s" style="color: #d14;">"r"</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="623" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
623
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<pre style="margin: 0;">+<span id="LC623" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">f</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;">GError</span><span class="p">(</span><span class="s" style="color: #d14;">"Error opening ID list file: %s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">chars</span><span class="p">());</span></span>
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624
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<pre style="margin: 0;">+<span id="LC624" class="line" lang="cpp"> <span class="n" style="color: #333;">loadIDlist</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">,</span> <span class="n" style="color: #333;">fltIDs</span><span class="p">);</span></span>
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625
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<pre style="margin: 0;">+<span id="LC625" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">fltIDs</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="626" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
626
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<pre style="margin: 0;">+<span id="LC626" class="line" lang="cpp"> <span class="n" style="color: #333;">GMessage</span><span class="p">(</span><span class="s" style="color: #d14;">"Warning: no IDs were loaded from file %s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">chars</span><span class="p">());</span></span>
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627
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<pre style="margin: 0;">+<span id="LC627" class="line" lang="cpp"> <span class="n" style="color: #333;">IDflt</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">idFlt_None</span><span class="p">;</span></span>
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624
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628
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<pre style="margin: 0;"> <span id="LC628" class="line" lang="cpp"> <span class="p">}</span></span>
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625
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<pre style="margin: 0;">-<span id="LC625" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC629" class="line" lang="cpp"> <span class="n" style="color: #333;">fclose</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC630" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC631" class="line" lang="cpp"> <span class="n" style="color: #333;">openfw</span><span class="p">(</span><span class="n" style="color: #333;">f_out</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">,</span> <span class="sc" style="color: #d14;">'o'</span><span class="p">);</span></span>
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627
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632
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<pre style="margin: 0;"> <span id="LC632" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//if (f_out==NULL) f_out=stdout;</span></span>
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633
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<pre style="margin: 0;"> <span id="LC633" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">gfasta</span><span class="p">.</span><span class="n" style="color: #333;">fastaPath</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="p">(</span><span class="n" style="color: #333;">validCDSonly</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">spliceCheck</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">getOpt</span><span class="p">(</span><span class="sc" style="color: #d14;">'w'</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;">args</span><span class="p">.</span><span class="n" style="color: #333;">getOpt</span><span class="p">(</span><span class="sc" style="color: #d14;">'x'</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;">args</span><span class="p">.</span><span class="n" style="color: #333;">getOpt</span><span class="p">(</span><span class="sc" style="color: #d14;">'y'</span><span class="p">)</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="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -630,19 +635,22 @@ int main(int argc, char* argv[]) {</td>
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635
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<pre style="margin: 0;"> <span id="LC635" class="line" lang="cpp"> <span class="n" style="color: #333;">openfw</span><span class="p">(</span><span class="n" style="color: #333;">f_w</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">,</span> <span class="sc" style="color: #d14;">'w'</span><span class="p">);</span></span>
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636
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<pre style="margin: 0;"> <span id="LC636" class="line" lang="cpp"> <span class="n" style="color: #333;">openfw</span><span class="p">(</span><span class="n" style="color: #333;">f_x</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">,</span> <span class="sc" style="color: #d14;">'x'</span><span class="p">);</span></span>
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637
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<pre style="margin: 0;"> <span id="LC637" class="line" lang="cpp"> <span class="n" style="color: #333;">openfw</span><span class="p">(</span><span class="n" style="color: #333;">f_y</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">,</span> <span class="sc" style="color: #d14;">'y'</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC638" class="line" lang="cpp"> <span class="n" style="color: #333;">openfw</span><span class="p">(</span><span class="n" style="color: #333;">f_j</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">,</span> <span class="sc" style="color: #d14;">'j'</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC639" class="line" lang="cpp"> <span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">getOpt</span><span class="p">(</span><span class="s" style="color: #d14;">"w-add"</span><span class="p">);</span></span>
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640
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<pre style="margin: 0;"> <span id="LC640" class="line" lang="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;">s</span><span class="p">.</span><span class="n" style="color: #333;">is_empty</span><span class="p">())</span> <span class="p">{</span></span>
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641
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<pre style="margin: 0;"> <span id="LC641" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">f_w</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;">GError</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: --w-add option requires -w option!</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC642" class="line" lang="cpp"> <span class="n" style="color: #333;">wPadding</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">asInt</span><span class="p">();</span></span>
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<pre style="margin: 0;"> <span id="LC643" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC644" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC645" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">f_w</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;">args</span><span class="p">.</span><span class="n" style="color: #333;">getOpt</span><span class="p">(</span><span class="s" style="color: #d14;">"w-nocds"</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC646" class="line" lang="cpp"> <span class="n" style="color: #333;">wfaNoCDS</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC647" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC648" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">f_out</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;">f_w</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;">f_x</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;">f_y</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="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">covInfo</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC649" class="line" lang="cpp"> <span class="n" style="color: #333;">f_out</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">stdout</span><span class="p">;</span></span>
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650
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<pre style="margin: 0;"> <span id="LC650" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC651" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//if (f_y!=NULL || f_x!=NULL) wCDSonly=true;</span></span>
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<pre style="margin: 0;"> <span id="LC652" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//useBadCDS=useBadCDS || (fgtfok==NULL && fgtfbad==NULL && f_y==NULL && f_x==NULL);</span></span>
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<pre style="margin: 0;"> <span id="LC653" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC645" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">numfiles</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">startNonOpt</span><span class="p">();</span></span>
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654
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<pre style="margin: 0;"> <span id="LC654" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//GList<GffObj> gfkept(false,true); //unsorted, free items on delete</span></span>
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<pre style="margin: 0;"> <span id="LC655" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">out_counter</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;">//number of records printed</span></span>
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<pre style="margin: 0;"> <span id="LC656" class="line" lang="cpp"></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">@@ -726,8 +734,8 @@ int main(int argc, char* argv[]) {</td>
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<pre style="margin: 0;"> <span id="LC734" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">firstLocusPrint</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC735" class="line" lang="cpp"> <span class="n" style="color: #333;">GffLocus</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">loc</span><span class="o" style="font-weight: 600;">=*</span><span class="p">(</span><span class="n" style="color: #333;">gdata</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">loci</span><span class="p">[</span><span class="n" style="color: #333;">l</span><span class="p">]);</span></span>
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<pre style="margin: 0;"> <span id="LC736" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//check all non-replaced transcripts in this locus:</span></span>
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<pre style="margin: 0;">-<span id="LC729" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">numvalid</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="LC730" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">idxfirstvalid</span><span class="o" style="font-weight: 600;">=-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC737" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">//</span>int numvalid=0;</span></span>
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<pre style="margin: 0;">+<span id="LC738" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">//</span>int idxfirstvalid=-1;</span></span>
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739
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<pre style="margin: 0;"> <span id="LC739" 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;">loc</span><span class="p">.</span><span class="n" style="color: #333;">rnas</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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740
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<pre style="margin: 0;"> <span id="LC740" 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="p">(</span><span class="n" style="color: #333;">loc</span><span class="p">.</span><span class="n" style="color: #333;">rnas</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]);</span></span>
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741
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<pre style="margin: 0;"> <span id="LC741" 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="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -752,15 +760,16 @@ int main(int argc, char* argv[]) {</td>
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<pre style="margin: 0;"> <span id="LC760" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//restore strand for dOvlSET</span></span>
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761
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<pre style="margin: 0;"> <span id="LC761" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">orig_strand</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">T_OSTRAND</span><span class="p">(</span><span class="n" style="color: #333;">t</span><span class="p">.</span><span class="n" style="color: #333;">udata</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="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">orig_strand</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;">t</span><span class="p">.</span><span class="n" style="color: #333;">strand</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">orig_strand</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC755" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC763" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/* -- transcripts are filtered upon loading</span></span>
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<pre style="margin: 0;"> <span id="LC764" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> if (process_transcript(gfasta, t)) {</span></span>
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<pre style="margin: 0;"> <span id="LC765" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> numvalid++;</span></span>
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<pre style="margin: 0;"> <span id="LC766" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> if (idxfirstvalid<0) idxfirstvalid=i;</span></span>
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<pre style="margin: 0;"> <span id="LC767" 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="LC768" 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="LC769" class="line" lang="cpp"> <span class="p">}</span> <span class="c1" style="color: #998; font-style: italic;">//for each transcript</span></span>
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<pre style="margin: 0;"> <span id="LC770" class="line" lang="cpp"></span>
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771
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<pre style="margin: 0;"> <span id="LC771" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">rnas_i</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC763" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">idxfirstvalid</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;">rnas_i</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">idxfirstvalid</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC772" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">//</span>if (idxfirstvalid>=0) rnas_i=idxfirstvalid;</span></span>
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<pre style="margin: 0;"> <span id="LC773" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">gfs_i</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC774" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">f_out</span><span class="p">)</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;">GStr</span> <span class="n" style="color: #333;">locname</span><span class="p">(</span><span class="s" style="color: #d14;">"RLOC_"</span><span class="p">);</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -775,7 +784,8 @@ int main(int argc, char* argv[]) {</td>
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784
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<pre style="margin: 0;"> <span id="LC784" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">firstGff3Print</span><span class="p">)</span> <span class="p">{</span> <span class="n" style="color: #333;">printGff3Header</span><span class="p">(</span><span class="n" style="color: #333;">f_out</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">);</span><span class="n" style="color: #333;">firstGff3Print</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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785
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<pre style="margin: 0;"> <span id="LC785" 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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786
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<pre style="margin: 0;"> <span id="LC786" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">firstLocusPrint</span><span class="p">)</span> <span class="p">{</span></span>
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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;">loc</span><span class="p">.</span><span class="n" style="color: #333;">print</span><span class="p">(</span><span class="n" style="color: #333;">f_out</span><span class="p">,</span> <span class="n" style="color: #333;">idxfirstvalid</span><span class="p">,</span> <span class="n" style="color: #333;">locname</span><span class="p">,</span> <span class="n" style="color: #333;">loctrack</span><span class="p">);</span></span>
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787
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<pre style="margin: 0;">+<span id="LC787" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//loc.print(f_out, idxfirstvalid, locname, loctrack);</span></span>
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788
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<pre style="margin: 0;">+<span id="LC788" class="line" lang="cpp"> <span class="n" style="color: #333;">loc</span><span class="p">.</span><span class="n" style="color: #333;">print</span><span class="p">(</span><span class="n" style="color: #333;">f_out</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">locname</span><span class="p">,</span> <span class="n" style="color: #333;">loctrack</span><span class="p">);</span></span>
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779
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789
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<pre style="margin: 0;"> <span id="LC789" class="line" lang="cpp"> <span class="n" style="color: #333;">firstLocusPrint</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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780
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790
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<pre style="margin: 0;"> <span id="LC790" class="line" lang="cpp"> <span class="p">}</span></span>
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781
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791
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<pre style="margin: 0;"> <span id="LC791" class="line" lang="cpp"> <span class="n" style="color: #333;">printGffObj</span><span class="p">(</span><span class="n" style="color: #333;">f_out</span><span class="p">,</span> <span class="n" style="color: #333;">loc</span><span class="p">.</span><span class="n" style="color: #333;">gfs</span><span class="p">[</span><span class="n" style="color: #333;">gfs_i</span><span class="p">],</span> <span class="n" style="color: #333;">locname</span><span class="p">,</span> <span class="n" style="color: #333;">exonPrinting</span><span class="p">,</span> <span class="n" style="color: #333;">out_counter</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="789" style="width: 35px; color: rgba(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="799" style="width: 35px; color: rgba(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">@@ -789,7 +799,8 @@ int main(int argc, char* argv[]) {</td>
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789
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799
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<pre style="margin: 0;"> <span id="LC799" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">firstGff3Print</span><span class="p">)</span> <span class="p">{</span> <span class="n" style="color: #333;">printGff3Header</span><span class="p">(</span><span class="n" style="color: #333;">f_out</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">);</span> <span class="n" style="color: #333;">firstGff3Print</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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790
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800
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<pre style="margin: 0;"> <span id="LC800" 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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791
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801
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<pre style="margin: 0;"> <span id="LC801" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">firstLocusPrint</span><span class="p">)</span> <span class="p">{</span></span>
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792
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<pre style="margin: 0;">-<span id="LC792" class="line" lang="cpp"> <span class="n" style="color: #333;">loc</span><span class="p">.</span><span class="n" style="color: #333;">print</span><span class="p">(</span><span class="n" style="color: #333;">f_out</span><span class="p">,</span> <span class="n" style="color: #333;">idxfirstvalid</span><span class="p">,</span> <span class="n" style="color: #333;">locname</span><span class="p">,</span> <span class="n" style="color: #333;">loctrack</span><span class="p">);</span></span>
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802
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<pre style="margin: 0;">+<span id="LC802" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//loc.print(f_out, idxfirstvalid, locname, loctrack);</span></span>
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803
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<pre style="margin: 0;">+<span id="LC803" class="line" lang="cpp"> <span class="n" style="color: #333;">loc</span><span class="p">.</span><span class="n" style="color: #333;">print</span><span class="p">(</span><span class="n" style="color: #333;">f_out</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">locname</span><span class="p">,</span> <span class="n" style="color: #333;">loctrack</span><span class="p">);</span></span>
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793
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804
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<pre style="margin: 0;"> <span id="LC804" class="line" lang="cpp"> <span class="n" style="color: #333;">firstLocusPrint</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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794
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805
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<pre style="margin: 0;"> <span id="LC805" class="line" lang="cpp"> <span class="p">}</span></span>
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795
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806
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<pre style="margin: 0;"> <span id="LC806" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="815" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -804,7 +815,7 @@ int main(int argc, char* argv[]) {</td>
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804
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815
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<pre style="margin: 0;"> <span id="LC815" class="line" lang="cpp"> <span class="p">}</span> <span class="c1" style="color: #998; font-style: italic;">//if Clustering enabled</span></span>
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805
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816
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<pre style="margin: 0;"> <span id="LC816" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">//no clustering</span></span>
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806
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817
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<pre style="margin: 0;"> <span id="LC817" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//not grouped into loci, print the rnas with their parents, if any</span></span>
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807
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<pre style="margin: 0;">-<span id="LC807" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">numvalid</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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818
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<pre style="margin: 0;">+<span id="LC818" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">//</span>int numvalid=0;</span></span>
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808
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819
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<pre style="margin: 0;"> <span id="LC819" 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;">g</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;">g</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">g_data</span><span class="p">.</span><span class="n" style="color: #333;">Count</span><span class="p">();</span><span class="n" style="color: #333;">g</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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809
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820
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<pre style="margin: 0;"> <span id="LC820" class="line" lang="cpp"> <span class="n" style="color: #333;">GenomicSeqData</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">gdata</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">g_data</span><span class="p">[</span><span class="n" style="color: #333;">g</span><span class="p">];</span></span>
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810
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821
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<pre style="margin: 0;"> <span id="LC821" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">firstGSeqHeader</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">fmtGFF3</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="815" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="826" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -815,6 +826,8 @@ int main(int argc, char* argv[]) {</td>
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815
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826
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<pre style="margin: 0;"> <span id="LC826" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//print other non-transcript (gene?) feature that might be there before t</span></span>
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816
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827
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<pre style="margin: 0;"> <span id="LC827" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">gfs_i</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">gdata</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">gfs</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="n" style="color: #333;">gdata</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">gfs</span><span class="p">[</span><span class="n" style="color: #333;">gfs_i</span><span class="p">]</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">start</span><span class="o" style="font-weight: 600;"><=</span><span class="n" style="color: #333;">t</span><span class="p">.</span><span class="n" style="color: #333;">start</span><span class="p">)</span> <span class="p">{</span></span>
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817
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828
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<pre style="margin: 0;"> <span id="LC828" 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;">gfst</span><span class="o" style="font-weight: 600;">=*</span><span class="p">(</span><span class="n" style="color: #333;">gdata</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">gfs</span><span class="p">[</span><span class="n" style="color: #333;">gfs_i</span><span class="p">]);</span></span>
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829
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<pre style="margin: 0;">+<span id="LC829" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">TFilters</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">gfst</span><span class="p">.</span><span class="n" style="color: #333;">isGene</span><span class="p">()</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">gfst</span><span class="p">.</span><span class="n" style="color: #333;">children</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="c1" style="color: #998; font-style: italic;">// gene with no children left, skip it if filters were applied</span></span>
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830
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<pre style="margin: 0;">+<span id="LC830" class="line" lang="cpp"> <span class="p">{</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">gfs_i</span><span class="p">;</span> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span> <span class="p">}</span></span>
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818
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831
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<pre style="margin: 0;"> <span id="LC831" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">T_PRINTABLE</span><span class="p">(</span><span class="n" style="color: #333;">gfst</span><span class="p">.</span><span class="n" style="color: #333;">udata</span><span class="p">)</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">//never printed</span></span>
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819
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832
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<pre style="margin: 0;"> <span id="LC832" class="line" lang="cpp"> <span class="n" style="color: #333;">T_NO_PRINT</span><span class="p">(</span><span class="n" style="color: #333;">gfst</span><span class="p">.</span><span class="n" style="color: #333;">udata</span><span class="p">);</span></span>
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820
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833
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<pre style="margin: 0;"> <span id="LC833" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">fmtGFF3</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="829" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -829,8 +842,8 @@ int main(int argc, char* argv[]) {</td>
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829
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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>
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830
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843
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<pre style="margin: 0;"> <span id="LC843" 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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831
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844
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<pre style="margin: 0;"> <span id="LC844" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">tdata</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">replaced_by</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;">continue</span><span class="p">;</span></span>
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832
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<pre style="margin: 0;">-<span id="LC832" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">process_transcript</span><span class="p">(</span><span class="n" style="color: #333;">gfasta</span><span class="p">,</span> <span class="n" style="color: #333;">t</span><span class="p">))</span> <span class="p">{</span></span>
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833
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<pre style="margin: 0;">-<span id="LC833" class="line" lang="cpp"> <span class="n" style="color: #333;">numvalid</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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845
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<pre style="margin: 0;">+<span id="LC845" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">//</span>if (process_transcript(gfasta, t)) {</span></span>
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846
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<pre style="margin: 0;">+<span id="LC846" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">//</span> numvalid++;</span></span>
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834
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847
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<pre style="margin: 0;"> <span id="LC847" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">f_out</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">T_PRINTABLE</span><span class="p">(</span><span class="n" style="color: #333;">t</span><span class="p">.</span><span class="n" style="color: #333;">udata</span><span class="p">)</span> <span class="p">)</span> <span class="p">{</span></span>
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835
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848
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<pre style="margin: 0;"> <span id="LC848" 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;">udata</span><span class="p">);</span></span>
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836
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849
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<pre style="margin: 0;"> <span id="LC849" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">fmtGFF3</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">fmtTable</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;">isTranscript</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="859" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="872" style="width: 35px; color: rgba(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">@@ -859,12 +872,14 @@ int main(int argc, char* argv[]) {</td>
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859
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872
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<pre style="margin: 0;"> <span id="LC872" 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>
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860
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873
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<pre style="margin: 0;"> <span id="LC873" class="line" lang="cpp"> <span class="p">}</span></span>
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861
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874
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<pre style="margin: 0;"> <span id="LC874" class="line" lang="cpp"> <span class="p">}</span><span class="c1" style="color: #998; font-style: italic;">//GFF/GTF output requested</span></span>
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862
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<pre style="margin: 0;">-<span id="LC862" class="line" lang="cpp"> <span class="p">}</span> <span class="c1" style="color: #998; font-style: italic;">//valid transcript</span></span>
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875
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<pre style="margin: 0;">+<span id="LC875" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">//</span>} //valid transcript</span></span>
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863
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876
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<pre style="margin: 0;"> <span id="LC876" class="line" lang="cpp"> <span class="p">}</span> <span class="c1" style="color: #998; font-style: italic;">//for each rna</span></span>
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864
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877
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<pre style="margin: 0;"> <span id="LC877" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//print the rest of the isolated pseudo/gene/region features not printed yet</span></span>
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865
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878
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<pre style="margin: 0;"> <span id="LC878" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">f_out</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">fmtGFF3</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">fmtTable</span><span class="p">))</span> <span class="p">{</span></span>
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866
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879
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<pre style="margin: 0;"> <span id="LC879" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">gfs_i</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">gdata</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">gfs</span><span class="p">.</span><span class="n" style="color: #333;">Count</span><span class="p">())</span> <span class="p">{</span></span>
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867
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880
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<pre style="margin: 0;"> <span id="LC880" 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;">gfst</span><span class="o" style="font-weight: 600;">=*</span><span class="p">(</span><span class="n" style="color: #333;">gdata</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">gfs</span><span class="p">[</span><span class="n" style="color: #333;">gfs_i</span><span class="p">]);</span></span>
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881
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<pre style="margin: 0;">+<span id="LC881" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">TFilters</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">gfst</span><span class="p">.</span><span class="n" style="color: #333;">isGene</span><span class="p">()</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">gfst</span><span class="p">.</span><span class="n" style="color: #333;">children</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="c1" style="color: #998; font-style: italic;">// gene with no children left, skip it if filters were applied</span></span>
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882
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<pre style="margin: 0;">+<span id="LC882" class="line" lang="cpp"> <span class="p">{</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">gfs_i</span><span class="p">;</span> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span> <span class="p">}</span></span>
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868
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883
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<pre style="margin: 0;"> <span id="LC883" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">T_PRINTABLE</span><span class="p">(</span><span class="n" style="color: #333;">gfst</span><span class="p">.</span><span class="n" style="color: #333;">udata</span><span class="p">)</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">//never printed</span></span>
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869
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884
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<pre style="margin: 0;"> <span id="LC884" class="line" lang="cpp"> <span class="n" style="color: #333;">T_NO_PRINT</span><span class="p">(</span><span class="n" style="color: #333;">gfst</span><span class="p">.</span><span class="n" style="color: #333;">udata</span><span class="p">);</span></span>
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870
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885
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<pre style="margin: 0;"> <span id="LC885" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">fmtGFF3</span><span class="p">)</span> <span class="p">{</span></span>
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<a href="https://salsa.debian.org/med-team/gffread/-/commit/8f84d6a4137aa1f105b971864eb5ea314c617754#ad76bfab75291d38945f9d9d0587235d3770a87c"><strong>prep_source.sh</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -14,7 +14,7 @@ libdir=$pack/gclib/</td>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="shell"><span class="s2" style="color: #d14;">cp LICENSE README.md gffread.cpp gff_utils.{h,cpp} </span><span class="nv" style="color: #008080;">$pack</span><span class="s2" style="color: #d14;">/</span></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="shell"><span class="s2" style="color: #d14;">sed 's|</span><span class="se" style="color: #d14;">\.\.</span><span class="s2" style="color: #d14;">/gclib|./gclib|' Makefile > </span><span class="nv" style="color: #008080;">$pack</span><span class="s2" style="color: #d14;">/Makefile</span></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="shell"><span class="s2" style="color: #d14;">cp ../gclib/{GVec,GList,GHash<span class="idiff left right">}.h</span>h </span><span class="nv" style="color: #008080;">$libdir</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="shell"><span class="s2" style="color: #d14;">cp ../gclib/{GVec,GList,GHash<span class="idiff left right">Map,khashl}.hh ../gclib/xxhash.</span>h </span><span class="nv" style="color: #008080;">$libdir</span></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="shell"><span class="s2" style="color: #d14;">cp ../gclib/{GArgs,GBase,gdna,GStr,gff,codons,GFaSeqGet,GFastaIndex}.{h,cpp} </span><span class="nv" style="color: #008080;">$libdir</span></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="shell"><span class="s2" style="color: #d14;">tar cvfz </span><span class="nv" style="color: #008080;">$pack</span><span class="s2" style="color: #d14;">.tar.gz </span><span class="nv" style="color: #008080;">$pack</span></span>
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20
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="shell"><span class="s2" style="color: #d14;">ls -l </span><span class="nv" style="color: #008080;">$pack</span><span class="s2" style="color: #d14;">.tar.gz</span></span>
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<li id="27ed1fc8ed3b072a62b0853848a75e935f58075b">
<a href="https://salsa.debian.org/med-team/gffread/-/commit/8f84d6a4137aa1f105b971864eb5ea314c617754#27ed1fc8ed3b072a62b0853848a75e935f58075b"><strong>tag_git.sh</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -3,12 +3,13 @@ git checkout master</td>
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="shell"><span class="nv" style="color: #008080;">ver</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span>fgrep <span class="s1" style="color: #d14;">'#define VERSION '</span> gffread.cpp<span class="si" style="color: #d14;">)</span></span>
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<td class="diff-line-num new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="shell"><span class="nv" style="color: #008080;">ver</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">ver</span><span class="p">#*\</span><span class="s2" style="color: #d14;">"}</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="shell"><span class="s2" style="color: #d14;">ver=</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">ver</span><span class="p">%%\</span><span class="s2" style="color: #d14;">"*}</span></span>
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6
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<td class="diff-line-num new_line old" data-linenumber="6" 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="LC6" class="line" lang="shell"><span class="s2" style="color: #d14;">git fetch --tags</span></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="shell"><span class="s2" style="color: #d14;"><span class="idiff left right">#</span>git fetch --tags</span></span>
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7
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<td class="diff-line-num new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="shell"><span class="s2" style="color: #d14;">if [[ "</span><span class="nv" style="color: #008080;">$1</span><span class="s2" style="color: #d14;">" == "</span><span class="nv" style="color: #008080;">delete</span><span class="s2" style="color: #d14;">" || "</span><span class="nv" style="color: #008080;">$1</span><span class="s2" style="color: #d14;">" == "</span><span class="nv" style="color: #008080;">del</span><span class="s2" style="color: #d14;">" ]]; then</span></span>
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8
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="shell"><span class="s2" style="color: #d14;"> echo "</span><span class="nv" style="color: #008080;">Deleting</span><span class="p"> tag v</span><span class="nv" style="color: #008080;">$ver</span><span class="p"> ..</span><span class="s2" style="color: #d14;">"</span></span>
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9
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<td class="diff-line-num new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="shell"><span class="s2" style="color: #d14;"> git tag -d v</span><span class="nv" style="color: #008080;">$ver</span></span>
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10
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<td class="diff-line-num new_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="shell"><span class="s2" style="color: #d14;"> git push origin :refs/tags/v</span><span class="nv" style="color: #008080;">$ver</span></span>
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11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="shell"><span class="s2" style="color: #d14;"> exit</span></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="shell"><span class="s2" style="color: #d14;">fi</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="shell"><span class="s2" style="color: #d14;">echo "</span><span class="nv" style="color: #008080;">Tagging</span><span class="p"> with v</span><span class="nv" style="color: #008080;">$ver</span><span class="s2" style="color: #d14;">"</span></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="shell"><span class="s2" style="color: #d14;">git tag -a "</span><span class="nv" style="color: #008080;">v$ver</span><span class="s2" style="color: #d14;">" -m "</span><span class="nv" style="color: #008080;">release</span><span class="p"> </span><span class="nv" style="color: #008080;">$ver</span><span class="s2" style="color: #d14;">"</span></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="shell"><span class="s2" style="color: #d14;">git push --tags</span></span></pre>
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