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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>
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<h4>
Commits:
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<ul>
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<strong><a href="https://salsa.debian.org/med-team/gffread/commit/5cd8d92443d463faca74bee7844219240412bc77">5cd8d924</a></strong>
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<span>by Andreas Tille</span>
<i>at 2019-08-08T09:54:00Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 0.11.4</pre>
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<h4>4 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#836efb6e25a091dcb4ff8e1dbb2f0be6a5cbf14c">
Makefile
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<li class="file-stats">
<a href="#2e62d67be9b972fb94be4079924f65c3df9a24ac">
gff_utils.cpp
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<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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<h4>Changes:</h4>
<li id="836efb6e25a091dcb4ff8e1dbb2f0be6a5cbf14c">
<a href="https://salsa.debian.org/med-team/gffread/commit/5cd8d92443d463faca74bee7844219240412bc77#836efb6e25a091dcb4ff8e1dbb2f0be6a5cbf14c"><strong>Makefile</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">@@ -10,7 +10,8 @@ LINKER := $(if $(LINKER),$(LINKER),g++)</td>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="make"><span class="nv" style="color: #008080;">LDFLAGS</span> <span class="o" style="font-weight: 600;">:=</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="o" style="font-weight: 600;">(</span><span class="k" style="font-weight: 600;">if</span> <span class="nv" style="color: #008080;">$(LDFLAGS)</span>,<span class="nv" style="color: #008080;">$(LDFLAGS)</span>,-g<span class="o" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="make"></span>
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<td class="diff-line-num old_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="make"><span class="nv" style="color: #008080;">BASEFLAGS</span> <span class="o" style="font-weight: 600;">:=</span> <span class="nt" style="color: #000080;">-Wall</span> <span class="nt" style="color: #000080;">-Wextra</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">SEARCHDIRS</span><span class="k" style="font-weight: 600;">}</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 old_line" data-linenumber="13" 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">
13
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<td class="diff-line-num new_line old" data-linenumber="13" 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="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="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="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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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 new new_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="make"> <span class="nt" style="color: #000080;">-std</span><span class="o" style="font-weight: 600;">=</span>c++0x <span class="nt" style="color: #000080;">-fno-exceptions</span> <span class="nt" style="color: #000080;">-fno-rtti</span></span>
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14
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<td class="diff-line-num new_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">
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="make"></span>
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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;">$(</span><span class="nb" style="color: #0086b3;">shell</span> <span class="nb" style="color: #0086b3;">expr</span> <span class="sb" style="color: #d14;">`</span>g++ <span class="nt" style="color: #000080;">-dumpversion</span> | <span class="nb" style="color: #0086b3;">cut</span> <span class="nt" style="color: #000080;">-f1</span> <span class="nt" style="color: #000080;">-d</span>.<span class="sb" style="color: #d14;">`</span> <span class="se" style="color: #d14;">\></span><span class="o" style="font-weight: 600;">=</span> 8<span class="nv" style="color: #008080;">)</span></span>
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<td class="diff-line-num new_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">ifeq</span> <span class="s2" style="color: #d14;">"$(GCCV8)"</span> <span class="s2" style="color: #d14;">"1"</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -21,14 +22,14 @@ CXXFLAGS := $(if $(CXXFLAGS),$(BASEFLAGS) $(CXXFLAGS),$(BASEFLAGS))</td>
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<td class="diff-line-num old_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="make"></span>
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<td class="diff-line-num new_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">ifneq</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">(,$(filter</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">%release</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">%static,</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$(MAKECMDGOALS)))</span></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="make"> <span class="c" style="color: #998; font-style: italic;"># -- release build</span></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="make"> <span class="nv" style="color: #008080;">CXXFLAGS</span> <span class="o" style="font-weight: 600;">:=</span> <span class="nt" style="color: #000080;">-g</span> <span class="nt" style="color: #000080;">-O3</span> <span class="nt" style="color: #000080;">-DNDEBUG</span> <span class="nt" style="color: #000080;"><span class="idiff left">-std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff right">c++0x </span><span class="nv" style="color: #008080;">$(CXXFLAGS)</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="make"> <span class="nv" style="color: #008080;">CXXFLAGS</span> <span class="o" style="font-weight: 600;">:=</span> <span class="nt" style="color: #000080;">-g</span> <span class="nt" style="color: #000080;">-O3</span> <span class="nt" style="color: #000080;">-DNDEBUG</span> <span class="nv" style="color: #008080;">$(CXXFLAGS)</span></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">else</span></span>
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<td class="diff-line-num new_line" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="make"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">ifneq</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">(,$(filter</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">%profile</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">%gprof</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">%prof,</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$(MAKECMDGOALS)))</span></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="make"> <span class="nv" style="color: #008080;">CXXFLAGS</span> <span class="o" style="font-weight: 600;">+=</span> <span class="nt" style="color: #000080;">-pg</span> <span class="nt" style="color: #000080;">-O0</span> <span class="nt" style="color: #000080;">-DNDEBUG</span><span class="idiff left"> </span><span class="nt" style="color: #000080;"><span class="idiff">-std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff right">c++0x</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="make"> <span class="nv" style="color: #008080;">CXXFLAGS</span> <span class="o" style="font-weight: 600;">+=</span> <span class="nt" style="color: #000080;">-pg</span> <span class="nt" style="color: #000080;">-O0</span> <span class="nt" style="color: #000080;">-DNDEBUG</span></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="make"> <span class="nv" style="color: #008080;">LDFLAGS</span> <span class="o" style="font-weight: 600;">+=</span> <span class="nt" style="color: #000080;">-pg</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="make"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">else</span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="make"> <span class="c" style="color: #998; font-style: italic;">#CXXFLAGS += -g -O0 -DNDEBUG</span></span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="make"> <span class="nv" style="color: #008080;">CXXFLAGS</span> <span class="o" style="font-weight: 600;">+=</span> <span class="nt" style="color: #000080;">-g</span> <span class="nt" style="color: #000080;">-O0</span> <span class="nt" style="color: #000080;">-DDEBUG</span> <span class="nt" style="color: #000080;">-D_DEBUG</span> <span class="nt" style="color: #000080;">-DGDEBUG</span><span class="idiff left"> </span><span class="nt" style="color: #000080;"><span class="idiff">-std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff right">c++0x</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="make"> <span class="nv" style="color: #008080;">CXXFLAGS</span> <span class="o" style="font-weight: 600;">+=</span> <span class="nt" style="color: #000080;">-g</span> <span class="nt" style="color: #000080;">-O0</span> <span class="nt" style="color: #000080;">-DDEBUG</span> <span class="nt" style="color: #000080;">-D_DEBUG</span> <span class="nt" style="color: #000080;">-DGDEBUG</span></span>
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32
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="make"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">endif</span></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="make"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">ifneq</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">(,$(filter</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">%memcheck</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">%memdebug,</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">$(MAKECMDGOALS)))</span></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="make"> <span class="c" style="color: #998; font-style: italic;">#use sanitizer in gcc 4.9+</span></span>
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<a href="https://salsa.debian.org/med-team/gffread/commit/5cd8d92443d463faca74bee7844219240412bc77#2e62d67be9b972fb94be4079924f65c3df9a24ac"><strong>gff_utils.cpp</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -3,7 +3,7 @@</td>
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">verbose</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">false</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">//same with GffReader::showWarnings and GffLoader::beVserbose</span></span>
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="cpp"></span>
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5
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//bool debugState=false;</span></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/*</span></span>
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7
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">void printTabFormat(FILE* f, GffObj* t) {</span></span>
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8
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8
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> static char dbuf[1024];</span></span>
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9
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> fprintf(f, "%s\t%s\t%c\t%d\t%d\t%d\t", t->getID(), t->getGSeqName(), t->strand, t->start, t->end, t->exons.Count());</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -26,6 +26,7 @@ void printTabFormat(FILE* f, GffObj* t) {</td>
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26
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> }</span></span>
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27
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> fprintf(f, "\n");</span></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">}</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">*/</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">printFasta</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">FILE</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">f</span><span class="p">,</span> <span class="n" style="color: #333;">GStr</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">defline</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">seqlen</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">useStar</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">seq</span><span class="o" style="font-weight: 600;">==</span><span class="nb" style="color: #0086b3;">NULL</span><span class="p">)</span> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="388" style="width: 35px; color: rgba(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">@@ -388,11 +389,11 @@ bool GffLoader::placeGf(GffObj* t, GenomicSeqData* gdata) {</td>
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388
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389
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<pre style="margin: 0;"> <span id="LC389" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//}</span></span>
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389
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390
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<pre style="margin: 0;"> <span id="LC390" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//GMessage("DBG>>Placing transcript %s(%d-%d, %d exons)\n", t->getID(), t->start, t->end, t->exons.Count());</span></span>
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391
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<pre style="margin: 0;"> <span id="LC391" class="line" lang="cpp"></span>
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391
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<pre style="margin: 0;">-<span id="LC391" 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="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;">t</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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<pre style="margin: 0;">+<span id="LC392" 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="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;">t</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">isTranscript</span><span class="p">()</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">trAdoption</span></span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC393" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">gidx</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="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC394" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">gidx</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;">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;">gidx</span><span class="p">]</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">end</span><span class="o" style="font-weight: 600;">>=</span><span class="n" style="color: #333;">t</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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<pre style="margin: 0;"> <span id="LC395" 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;">g</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">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;">gidx</span><span class="p">]);</span></span>
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<pre style="margin: 0;">-<span id="LC395" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//find a container gene object for this transcript</span></span>
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<pre style="margin: 0;">+<span id="LC396" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//<span class="idiff left right">try to </span>find a container gene object for this transcript</span></span>
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397
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<pre style="margin: 0;"> <span id="LC397" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//if (g.isGene() && t->strand==g.strand && exonOverlap2Gene(t, g)) {</span></span>
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398
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<pre style="margin: 0;"> <span id="LC398" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">g</span><span class="p">.</span><span class="n" style="color: #333;">isGene</span><span class="p">()</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">t</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">strand</span><span class="o" style="font-weight: 600;">==</span><span class="sc" style="color: #d14;">'.'</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">t</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;">g</span><span class="p">.</span><span class="n" style="color: #333;">strand</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">g</span><span class="p">.</span><span class="n" style="color: #333;">exons</span><span class="p">.</span><span class="n" style="color: #333;">Count</span><span class="p">()</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">0</span></span>
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<pre style="margin: 0;"> <span id="LC399" class="line" lang="cpp"> <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;">start</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;">start</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;">end</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;">end</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -403,7 +404,7 @@ bool GffLoader::placeGf(GffObj* t, GenomicSeqData* gdata) {</td>
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<pre style="margin: 0;"> <span id="LC404" class="line" lang="cpp"> <span class="n" style="color: #333;">tdata</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">GTData</span><span class="p">(</span><span class="n" style="color: #333;">t</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">//additional transcript data</span></span>
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<pre style="margin: 0;"> <span id="LC405" class="line" lang="cpp"> <span class="n" style="color: #333;">gdata</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">tdata</span><span class="p">.</span><span class="n" style="color: #333;">Add</span><span class="p">(</span><span class="n" style="color: #333;">tdata</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC406" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC406" class="line" lang="cpp"> <span class="k" style="font-weight: 600;"><span class="idiff left">if</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">t</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">parent</span></span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">NULL</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">t</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;">g</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC407" 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;">parent</span><span class="o" style="font-weight: 600;">=&</span><span class="n" style="color: #333;">g</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC408" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//disable printing of gene if transcriptsOnly and --keep-genes wasn't given</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;">transcriptsOnly</span> <span class="o" style="font-weight: 600;">&&</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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409
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<pre style="margin: 0;"> <span id="LC410" class="line" lang="cpp"> <span class="n" style="color: #333;">T_NO_PRINT</span><span class="p">(</span><span class="n" style="color: #333;">g</span><span class="p">.</span><span class="n" style="color: #333;">udata</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">//tag it as non-printable</span></span>
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<a href="https://salsa.debian.org/med-team/gffread/commit/5cd8d92443d463faca74bee7844219240412bc77#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">@@ -565,6 +565,7 @@ class GffLoader {</td>
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<pre style="margin: 0;"> <span id="LC565" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">BEDinput</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="LC566" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">TLFinput</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="LC567" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">keepGenes</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="LC568" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">trAdoption</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;">//orphan transcript adoption by the container gene</span></span>
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<pre style="margin: 0;"> <span id="LC569" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">keepGff3Comments</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="LC570" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">sortRefsAlpha</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="LC571" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">doCluster</span><span class="o" style="font-weight: 600;">:</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -628,7 +629,7 @@ class GffLoader {</td>
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<pre style="margin: 0;"> <span id="LC629" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC630" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">printFasta</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">FILE</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">f</span><span class="p">,</span> <span class="n" style="color: #333;">GStr</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">defline</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">seqlen</span><span class="o" style="font-weight: 600;">=-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">useStar</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">false</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC631" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC631" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">printTabFormat</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;">t</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC632" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">//</span>void printTabFormat(FILE* f, GffObj* t);</span></span>
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<pre style="margin: 0;"> <span id="LC633" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC634" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">//"position" a given coordinate x within a list of transcripts sorted by their start (lowest)</span></span>
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<pre style="margin: 0;"> <span id="LC635" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">//coordinate, using quick-search; the returned int is the list index of the closest *higher*</span></span>
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<a href="https://salsa.debian.org/med-team/gffread/commit/5cd8d92443d463faca74bee7844219240412bc77#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">@@ -4,16 +4,19 @@</td>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#define __STDC_FORMAT_MACROS</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <inttypes.h></span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#define VERSION "0.11.<span class="idiff left right">2</span>"</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#define VERSION "0.11.<span class="idiff left right">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 <input_gff> [-g <genomic_seqs_fasta> | <dir>][-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<span class="idiff left right">.gff>] [-t <t</span>name>] [-r [[<strand>]<chr>:]<start>..<end> [-R]]\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<span class="idiff left right">>] [-t <track</span>name>] [-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>] [--<span class="idiff left right">sort-by <refseq_list.txt>] </span>\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>] [--<span class="idiff left right">bed] [--table <attrlist>] [--sort-by <refseq_list.txt>]</span>\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="LC15" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"> Filter and convert GFF3/GTF2 records, extract corresponding sequences etc.\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;"> By default (i.e. without -O) only process transcripts, ignore other features.\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;"> 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="LC16" 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="LC17" 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="LC18" 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="LC19" 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="LC20" 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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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -39,7 +42,7 @@ Sorting: (by default, chromosomes are kept in the order they were found)\n\</td>
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<pre style="margin: 0;"> <span id="LC42" 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="LC43" 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="LC44" 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="LC42" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"> -F <span class="idiff left right">attempt to preserve all GFF attributes preservation</span>\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 all GFF attributes (for non-exon features)</span>\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;"> --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="LC47" 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="LC48" 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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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -90,6 +93,8 @@ Output options:\n\</td>
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<pre style="margin: 0;"> <span id="LC93" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"> \"exon\" features\n\</span></span>
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<pre style="margin: 0;"> <span id="LC94" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"> --gene2exon: for single-line genes not parenting any transcripts, add an\n\</span></span>
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<pre style="margin: 0;"> <span id="LC95" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"> exon feature spanning the entire gene (treat it as a transcript)\n\</span></span>
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"> --t-adopt: try to find a parent gene overlapping/containing a transcript\n\</span></span>
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"> that does not have any explicit gene Parent\n\</span></span>
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<pre style="margin: 0;"> <span id="LC98" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"> -D decode url encoded characters within attributes\n\</span></span>
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"> -Z merge very close exons into a single exon (when intron size<4)\n\</span></span>
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<pre style="margin: 0;"> <span id="LC100" 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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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -109,16 +114,19 @@ Output options:\n\</td>
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<pre style="margin: 0;"> <span id="LC114" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"> WARNING: all GFF records on reference sequences whose original IDs\n\</span></span>
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<pre style="margin: 0;"> <span id="LC115" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"> are not found in the 1st column of this table will be discarded!\n\</span></span>
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<pre style="margin: 0;"> <span id="LC116" 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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<pre style="margin: 0;">-<span id="LC112" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"> -o print the GFF records to <outfile.gff> (those that passed any\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;"> given filters). Use -o- to enable printing of to stdout\n\</span></span>
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<pre style="margin: 0;">-<span id="LC114" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"> -T for -o, output will be GTF instead of GFF3\n\</span></span>
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<pre style="margin: 0;">-<span id="LC115" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"> --bed for -o, output BED format instead of GFF3\n\</span></span>
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<td class="diff-line-num old old_line" data-linenumber="116" 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="LC116" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"> --tlf for -o, output \"transcript line format\" which is like GFF\n\</span></span>
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<pre style="margin: 0;">+<span id="LC117" 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="LC118" 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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<td class="diff-line-num new new_line" data-linenumber="119" style="width: 35px; color: rgba(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="LC119" 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="LC120" 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="LC121" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"> but exons, CDS features and related data are stored as 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;"> attributes in the transcript feature line, like this:\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;"> exoncount=N;exons=<exons>;CDSphase=<N>;CDS=<CDScoords> \n\</span></span>
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<pre style="margin: 0;">-<span id="LC120" 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="diff-line-num old old_line" data-linenumber="121" 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="LC121" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"> <CDScoords> is CDS_start:CDS_end coordinates or a list like <exons>;\n\</span></span>
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<pre style="margin: 0;">+<span id="LC124" 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="diff-line-num new new_line" data-linenumber="125" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"> <CDScoords> is CDS_start:CDS_end coordinates or a list like <exons>\n\</span></span>
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<td class="diff-line-num new new_line" data-linenumber="126" style="width: 35px; color: rgba(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="LC126" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"> --table output a simple tab delimited format instead of GFF, with columns\n\</span></span>
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<td class="diff-line-num new old_line" data-linenumber="122" style="width: 35px; color: rgba(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="LC127" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"> having the values of GFF attributes given in <attrlist>; special\n\</span></span>
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<td class="diff-line-num new new_line" data-linenumber="128" style="width: 35px; color: rgba(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="LC128" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"> pseudo-attributes (prefixed by @) are recognized:\n\</span></span>
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"> @chr, @start, @end, @strand, @numexons, @exons, @cds, @covlen, @cdslen\n\</span></span>
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122
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<pre style="margin: 0;"> <span id="LC130" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"> -v,-E expose (warn about) duplicate transcript IDs and other potential\n\</span></span>
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123
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131
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<pre style="margin: 0;"> <span id="LC131" 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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124
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132
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<pre style="margin: 0;"> <span id="LC132" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">"</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</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">@@ -149,6 +157,30 @@ class RefTran {</td>
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149
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157
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<pre style="margin: 0;"> <span id="LC157" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC158" class="line" lang="cpp"><span class="p">};</span></span>
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<pre style="margin: 0;"> <span id="LC159" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="cpp"><span class="k" style="font-weight: 600;">enum</span> <span class="n" style="color: #333;">ETableFieldType</span> <span class="p">{</span></span>
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161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="cpp"> <span class="n" style="color: #333;">ctfGFF_Attr</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="c1" style="color: #998; font-style: italic;">// attribute name as is</span></span>
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162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="cpp"> <span class="n" style="color: #333;">ctfGFF_ID</span><span class="p">,</span> <span class="c1" style="color: #998; font-style: italic;">//ID or @id</span></span>
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163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="cpp"> <span class="n" style="color: #333;">ctfGFF_Parent</span><span class="p">,</span> <span class="c1" style="color: #998; font-style: italic;">//Parent or @parent</span></span>
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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="cpp"> <span class="n" style="color: #333;">ctfGFF_chr</span><span class="p">,</span> <span class="c1" style="color: #998; font-style: italic;">//@chr</span></span>
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165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="cpp"> <span class="n" style="color: #333;">ctfGFF_feature</span><span class="p">,</span> <span class="c1" style="color: #998; font-style: italic;">//@feature</span></span>
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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="cpp"> <span class="n" style="color: #333;">ctfGFF_start</span><span class="p">,</span> <span class="c1" style="color: #998; font-style: italic;">//@start</span></span>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="cpp"> <span class="n" style="color: #333;">ctfGFF_end</span><span class="p">,</span> <span class="c1" style="color: #998; font-style: italic;">//@end</span></span>
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="cpp"> <span class="n" style="color: #333;">ctfGFF_strand</span><span class="p">,</span> <span class="c1" style="color: #998; font-style: italic;">//@strand</span></span>
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="cpp"> <span class="n" style="color: #333;">ctfGFF_numexons</span><span class="p">,</span> <span class="c1" style="color: #998; font-style: italic;">//@numexons</span></span>
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170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="cpp"> <span class="n" style="color: #333;">ctfGFF_exons</span><span class="p">,</span> <span class="c1" style="color: #998; font-style: italic;">//@exons</span></span>
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171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="cpp"> <span class="n" style="color: #333;">ctfGFF_cds</span><span class="p">,</span> <span class="c1" style="color: #998; font-style: italic;">//@cds</span></span>
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172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="cpp"> <span class="n" style="color: #333;">ctfGFF_covlen</span><span class="p">,</span> <span class="c1" style="color: #998; font-style: italic;">//@covlen</span></span>
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173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="cpp"> <span class="n" style="color: #333;">ctfGFF_cdslen</span><span class="c1" style="color: #998; font-style: italic;">//@cdslen</span></span>
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174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="cpp"><span class="p">};</span></span>
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175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="cpp"></span>
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176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="cpp"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">CTableField</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="cpp"> <span class="nl">public:</span></span>
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178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="cpp"> <span class="n" style="color: #333;">ETableFieldType</span> <span class="n" style="color: #333;">type</span><span class="p">;</span></span>
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179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="cpp"> <span class="n" style="color: #333;">GStr</span> <span class="n" style="color: #333;">name</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">//only for type ctfGFF_Attr</span></span>
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180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="cpp"> <span class="n" style="color: #333;">CTableField</span><span class="p">(</span><span class="n" style="color: #333;">ETableFieldType</span> <span class="n" style="color: #333;">atype</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">ctfGFF_Attr</span><span class="p">)</span><span class="o" style="font-weight: 600;">:</span><span class="n" style="color: #333;">type</span><span class="p">(</span><span class="n" style="color: #333;">atype</span><span class="p">)</span> <span class="p">{</span> <span class="p">}</span></span>
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181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="cpp"> <span class="n" style="color: #333;">CTableField</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;">attrname</span><span class="p">)</span><span class="o" style="font-weight: 600;">:</span><span class="n" style="color: #333;">type</span><span class="p">(</span><span class="n" style="color: #333;">ctfGFF_Attr</span><span class="p">),</span><span class="n" style="color: #333;">name</span><span class="p">(</span><span class="n" style="color: #333;">attrname</span><span class="p">)</span> <span class="p">{</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="cpp"><span class="p">};</span></span>
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183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="cpp"></span>
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152
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184
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<pre style="margin: 0;"> <span id="LC184" 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;">ffasta</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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153
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185
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<pre style="margin: 0;"> <span id="LC185" 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_in</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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154
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186
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<pre style="margin: 0;"> <span id="LC186" 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_out</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="173" style="width: 35px; color: rgba(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="205" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -173,7 +205,7 @@ bool covInfo=false; // --cov-info : only report genome coverage</td>
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173
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205
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<pre style="margin: 0;"> <span id="LC205" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//bool sortAlpha=false;</span></span>
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174
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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;">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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175
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<pre style="margin: 0;"> <span id="LC207" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//bool keepRefOrder=false; //sort within chromosomes, but follow the input chromosome order -- default!</span></span>
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176
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<pre style="margin: 0;">-<span id="LC176" class="line" lang="cpp"></span>
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208
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="cpp"><span class="n" style="color: #333;">GStr</span> <span class="n" style="color: #333;">tableFormat</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">//list of "attributes" to print in tab delimited format</span></span>
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177
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<pre style="margin: 0;"> <span id="LC209" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//bool NoPseudo=false;</span></span>
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178
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<pre style="margin: 0;"> <span id="LC210" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">spliceCheck</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;">//only known splice-sites</span></span>
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179
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211
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<pre style="margin: 0;"> <span id="LC211" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">decodeChars</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;">//decode url-encoded chars in attrs (-D)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="225" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -193,6 +225,7 @@ bool fmtGFF3=true; //default output: GFF3</td>
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193
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225
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<pre style="margin: 0;"> <span id="LC225" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">fmtGTF</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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226
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<pre style="margin: 0;"> <span id="LC226" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">fmtBED</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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195
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227
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<pre style="margin: 0;"> <span id="LC227" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">fmtTLF</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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228
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">fmtTable</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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196
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229
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<pre style="margin: 0;"> <span id="LC229" 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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197
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230
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<pre style="margin: 0;"> <span id="LC230" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//bool protmap=false;</span></span>
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198
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231
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<pre style="margin: 0;"> <span id="LC231" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">multiExon</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="diff-line-num unfold js-unfold old_line" data-linenumber="221" style="width: 35px; color: rgba(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="254" style="width: 35px; color: rgba(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">@@ -221,6 +254,9 @@ GHash<GeneInfo> gene_ids;</td>
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221
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<pre style="margin: 0;"> <span id="LC254" 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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<pre style="margin: 0;"> <span id="LC255" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//bool verbose=false;</span></span>
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<pre style="margin: 0;"> <span id="LC256" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC257" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC258" 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 class="c1" style="color: #998; font-style: italic;">//table output format fields</span></span>
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<pre style="margin: 0;">+<span id="LC259" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC260" 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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225
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261
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<pre style="margin: 0;"> <span id="LC261" 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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226
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<pre style="margin: 0;"> <span id="LC262" 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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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="251" style="width: 35px; color: rgba(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="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="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -251,6 +287,50 @@ void loadSeqInfo(FILE* f, GHash<SeqInfo> &si) {</td>
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251
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<pre style="margin: 0;"> <span id="LC287" 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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252
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<pre style="margin: 0;"> <span id="LC288" class="line" lang="cpp"><span class="p">}</span></span>
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253
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<pre style="margin: 0;"> <span id="LC289" class="line" lang="cpp"></span>
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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;">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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291
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<pre style="margin: 0;">+<span id="LC291" 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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292
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<pre style="margin: 0;">+<span id="LC292" 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 new old_line" data-linenumber="254" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="293" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
293
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<pre style="margin: 0;">+<span id="LC293" class="line" lang="cpp"> <span class="n" style="color: #333;">specialFields</span><span class="p">.</span><span class="n" style="color: #333;">Add</span><span class="p">(</span><span class="s" style="color: #d14;">"chr"</span><span class="p">,</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">ETableFieldType</span><span class="p">(</span><span class="n" style="color: #333;">ctfGFF_chr</span><span class="p">));</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="254" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="294" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
294
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<pre style="margin: 0;">+<span id="LC294" class="line" lang="cpp"> <span class="n" style="color: #333;">specialFields</span><span class="p">.</span><span class="n" style="color: #333;">Add</span><span class="p">(</span><span class="s" style="color: #d14;">"id"</span><span class="p">,</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">ETableFieldType</span><span class="p">(</span><span class="n" style="color: #333;">ctfGFF_ID</span><span class="p">));</span></span>
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<td class="diff-line-num new old_line" data-linenumber="254" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="295" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
295
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<pre style="margin: 0;">+<span id="LC295" class="line" lang="cpp"> <span class="n" style="color: #333;">specialFields</span><span class="p">.</span><span class="n" style="color: #333;">Add</span><span class="p">(</span><span class="s" style="color: #d14;">"parent"</span><span class="p">,</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">ETableFieldType</span><span class="p">(</span><span class="n" style="color: #333;">ctfGFF_Parent</span><span class="p">));</span></span>
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<td class="diff-line-num new old_line" data-linenumber="254" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="296" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
296
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC296" class="line" lang="cpp"> <span class="n" style="color: #333;">specialFields</span><span class="p">.</span><span class="n" style="color: #333;">Add</span><span class="p">(</span><span class="s" style="color: #d14;">"feature"</span><span class="p">,</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">ETableFieldType</span><span class="p">(</span><span class="n" style="color: #333;">ctfGFF_feature</span><span class="p">));</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="254" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="297" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
297
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<pre style="margin: 0;">+<span id="LC297" class="line" lang="cpp"> <span class="n" style="color: #333;">specialFields</span><span class="p">.</span><span class="n" style="color: #333;">Add</span><span class="p">(</span><span class="s" style="color: #d14;">"start"</span><span class="p">,</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">ETableFieldType</span><span class="p">(</span><span class="n" style="color: #333;">ctfGFF_start</span><span class="p">));</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="254" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="298" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
298
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<pre style="margin: 0;">+<span id="LC298" 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;">new</span> <span class="n" style="color: #333;">ETableFieldType</span><span class="p">(</span><span class="n" style="color: #333;">ctfGFF_end</span><span class="p">));</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="254" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="299" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
299
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<pre style="margin: 0;">+<span id="LC299" class="line" lang="cpp"> <span class="n" style="color: #333;">specialFields</span><span class="p">.</span><span class="n" style="color: #333;">Add</span><span class="p">(</span><span class="s" style="color: #d14;">"strand"</span><span class="p">,</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">ETableFieldType</span><span class="p">(</span><span class="n" style="color: #333;">ctfGFF_strand</span><span class="p">));</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="254" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="300" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
300
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC300" class="line" lang="cpp"> <span class="n" style="color: #333;">specialFields</span><span class="p">.</span><span class="n" style="color: #333;">Add</span><span class="p">(</span><span class="s" style="color: #d14;">"numexons"</span><span class="p">,</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">ETableFieldType</span><span class="p">(</span><span class="n" style="color: #333;">ctfGFF_numexons</span><span class="p">));</span></span>
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<td class="diff-line-num new old_line" data-linenumber="254" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="301" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
301
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<pre style="margin: 0;">+<span id="LC301" class="line" lang="cpp"> <span class="n" style="color: #333;">specialFields</span><span class="p">.</span><span class="n" style="color: #333;">Add</span><span class="p">(</span><span class="s" style="color: #d14;">"exons"</span><span class="p">,</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">ETableFieldType</span><span class="p">(</span><span class="n" style="color: #333;">ctfGFF_exons</span><span class="p">));</span></span>
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<td class="diff-line-num new old_line" data-linenumber="254" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="302" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
302
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<pre style="margin: 0;">+<span id="LC302" class="line" lang="cpp"> <span class="n" style="color: #333;">specialFields</span><span class="p">.</span><span class="n" style="color: #333;">Add</span><span class="p">(</span><span class="s" style="color: #d14;">"cds"</span><span class="p">,</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">ETableFieldType</span><span class="p">(</span><span class="n" style="color: #333;">ctfGFF_cds</span><span class="p">));</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="254" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="303" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
303
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC303" class="line" lang="cpp"> <span class="n" style="color: #333;">specialFields</span><span class="p">.</span><span class="n" style="color: #333;">Add</span><span class="p">(</span><span class="s" style="color: #d14;">"covlen"</span><span class="p">,</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">ETableFieldType</span><span class="p">(</span><span class="n" style="color: #333;">ctfGFF_covlen</span><span class="p">));</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="254" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="304" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
304
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC304" class="line" lang="cpp"> <span class="n" style="color: #333;">specialFields</span><span class="p">.</span><span class="n" style="color: #333;">Add</span><span class="p">(</span><span class="s" style="color: #d14;">"cdslen"</span><span class="p">,</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">ETableFieldType</span><span class="p">(</span><span class="n" style="color: #333;">ctfGFF_cdslen</span><span class="p">));</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="254" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="305" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
305
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<pre style="margin: 0;">+<span id="LC305" class="line" lang="cpp"></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="254" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="306" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
306
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<pre style="margin: 0;">+<span id="LC306" 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>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="254" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="307" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
307
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<pre style="margin: 0;">+<span id="LC307" 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>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="254" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="308" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
308
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<pre style="margin: 0;">+<span id="LC308" 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>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="254" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="309" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
309
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC309" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">w</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span><span class="o" style="font-weight: 600;">==</span><span class="sc" style="color: #d14;">'@'</span><span class="p">)</span> <span class="p">{</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="254" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="310" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
310
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<pre style="margin: 0;">+<span id="LC310" class="line" lang="cpp"> <span class="n" style="color: #333;">w</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">w</span><span class="p">.</span><span class="n" style="color: #333;">substr</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="254" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="311" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
311
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<pre style="margin: 0;">+<span id="LC311" class="line" lang="cpp"> <span class="n" style="color: #333;">ETableFieldType</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">v</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">specialFields</span><span class="p">.</span><span class="n" style="color: #333;">Find</span><span class="p">(</span><span class="n" style="color: #333;">w</span><span class="p">.</span><span class="n" style="color: #333;">chars</span><span class="p">());</span></span>
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<td class="diff-line-num new new_line" data-linenumber="312" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
312
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<pre style="margin: 0;">+<span id="LC312" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">v</span><span class="o" style="font-weight: 600;">!=</span><span class="nb" style="color: #0086b3;">NULL</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="313" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
313
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<pre style="margin: 0;">+<span id="LC313" class="line" lang="cpp"> <span class="n" style="color: #333;">CTableField</span> <span class="n" style="color: #333;">tcol</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">v</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="314" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
314
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<pre style="margin: 0;">+<span id="LC314" class="line" lang="cpp"> <span class="n" style="color: #333;">tableCols</span><span class="p">.</span><span class="n" style="color: #333;">Add</span><span class="p">(</span><span class="n" style="color: #333;">tcol</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="315" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
315
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<pre style="margin: 0;">+<span id="LC315" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="316" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
316
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<pre style="margin: 0;">+<span id="LC316" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">GMessage</span><span class="p">(</span><span class="s" style="color: #d14;">"Warning: table field '@%s' not recognized!</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;">w</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="317" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
317
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<pre style="margin: 0;">+<span id="LC317" 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 new new_line" data-linenumber="318" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
318
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<pre style="margin: 0;">+<span id="LC318" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="319" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
319
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<pre style="margin: 0;">+<span id="LC319" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">w</span><span class="o" style="font-weight: 600;">==</span><span class="s" style="color: #d14;">"ID"</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="320" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
320
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<pre style="margin: 0;">+<span id="LC320" class="line" lang="cpp"> <span class="n" style="color: #333;">CTableField</span> <span class="n" style="color: #333;">tcol</span><span class="p">(</span><span class="n" style="color: #333;">ctfGFF_ID</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="321" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
321
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<pre style="margin: 0;">+<span id="LC321" class="line" lang="cpp"> <span class="n" style="color: #333;">tableCols</span><span class="p">.</span><span class="n" style="color: #333;">Add</span><span class="p">(</span><span class="n" style="color: #333;">tcol</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="322" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
322
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<pre style="margin: 0;">+<span id="LC322" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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323
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<pre style="margin: 0;">+<span id="LC323" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="324" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
324
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<pre style="margin: 0;">+<span id="LC324" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">w</span><span class="o" style="font-weight: 600;">==</span><span class="s" style="color: #d14;">"Parent"</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="325" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
325
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<pre style="margin: 0;">+<span id="LC325" class="line" lang="cpp"> <span class="n" style="color: #333;">CTableField</span> <span class="n" style="color: #333;">tcol</span><span class="p">(</span><span class="n" style="color: #333;">ctfGFF_Parent</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="326" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
326
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<pre style="margin: 0;">+<span id="LC326" class="line" lang="cpp"> <span class="n" style="color: #333;">tableCols</span><span class="p">.</span><span class="n" style="color: #333;">Add</span><span class="p">(</span><span class="n" style="color: #333;">tcol</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="327" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
327
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<pre style="margin: 0;">+<span id="LC327" 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 new new_line" data-linenumber="328" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
328
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<pre style="margin: 0;">+<span id="LC328" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="329" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
329
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<pre style="margin: 0;">+<span id="LC329" class="line" lang="cpp"> <span class="n" style="color: #333;">CTableField</span> <span class="n" style="color: #333;">col</span><span class="p">(</span><span class="n" style="color: #333;">w</span><span class="p">);</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="330" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
330
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<pre style="margin: 0;">+<span id="LC330" class="line" lang="cpp"> <span class="n" style="color: #333;">tableCols</span><span class="p">.</span><span class="n" style="color: #333;">Add</span><span class="p">(</span><span class="n" style="color: #333;">col</span><span class="p">);</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="331" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
331
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<pre style="margin: 0;">+<span id="LC331" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="332" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
332
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<pre style="margin: 0;">+<span id="LC332" class="line" lang="cpp"><span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="333" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
333
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<pre style="margin: 0;">+<span id="LC333" class="line" lang="cpp"></span>
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334
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<pre style="margin: 0;"> <span id="LC334" 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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<pre style="margin: 0;"> <span id="LC335" 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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336
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<pre style="margin: 0;"> <span id="LC336" 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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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="347" style="width: 35px; color: rgba(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="427" style="width: 35px; color: rgba(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">@@ -347,16 +427,6 @@ bool process_transcript(GFastaDb& gfasta, GffObj& gffrec) {</td>
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347
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427
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<pre style="margin: 0;"> <span id="LC427" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//returns true if the transcript passed the filter</span></span>
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348
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428
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<pre style="margin: 0;"> <span id="LC428" 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;">gname</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;">getGeneName</span><span class="p">();</span></span>
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349
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429
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<pre style="margin: 0;"> <span id="LC429" 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="nb" style="color: #0086b3;">NULL</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;">gffrec</span><span class="p">.</span><span class="n" style="color: #333;">getGeneID</span><span class="p">();</span></span>
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<pre style="margin: 0;">-<span id="LC350" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/*</span></span>
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351
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<pre style="margin: 0;">-<span id="LC351" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> if (f_out) { //remove transcript_name, convert it to Name for GFF3 output -- should we?</span></span>
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352
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<pre style="margin: 0;">-<span id="LC352" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> const char* tname=NULL;</span></span>
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<pre style="margin: 0;">-<span id="LC353" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> if ((tname=gffrec.getAttr("transcript_name"))!=NULL &&</span></span>
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<pre style="margin: 0;">-<span id="LC354" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> gffrec.getAttr("Name")==NULL) {</span></span>
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<pre style="margin: 0;">-<span id="LC355" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> gffrec.addAttr("Name", tname);</span></span>
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<pre style="margin: 0;">-<span id="LC356" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> gffrec.removeAttr("transcript_name");</span></span>
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<pre style="margin: 0;">-<span id="LC357" 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="LC358" 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="LC359" 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="LC430" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">ensembl_convert</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">startsWith</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="s" style="color: #d14;">"ENS"</span><span class="p">))</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC431" class="line" lang="cpp"> <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;">biotype</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;">getAttr</span><span class="p">(</span><span class="s" style="color: #d14;">"gene_biotype"</span><span class="p">);</span></span>
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432
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<pre style="margin: 0;"> <span id="LC432" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">biotype</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="676" style="width: 35px; color: rgba(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="746" style="width: 35px; color: rgba(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">@@ -676,15 +746,15 @@ bool process_transcript(GFastaDb& gfasta, GffObj& gffrec) {</td>
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676
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<pre style="margin: 0;"> <span id="LC746" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC747" class="line" lang="cpp"></span>
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678
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<pre style="margin: 0;"> <span id="LC748" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">openfw</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="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">f</span><span class="p">,</span> <span class="n" style="color: #333;">GArgs</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">args</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">opt</span><span class="p">)</span> <span class="p">{</span></span>
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679
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<pre style="margin: 0;">-<span id="LC679" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">GStr</span> <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="n" style="color: #333;">opt</span><span class="p">);</span></span>
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680
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<pre style="margin: 0;">-<span id="LC680" 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="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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<pre style="margin: 0;">-<span id="LC681" 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;">s</span><span class="o" style="font-weight: 600;">==</span><span class="sc" style="color: #d14;">'-'</span><span class="p">)</span></span>
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682
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<pre style="margin: 0;">-<span id="LC682" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">f</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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683
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<pre style="margin: 0;">-<span id="LC683" class="line" lang="cpp"><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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684
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<pre style="margin: 0;">-<span id="LC684" class="line" lang="cpp"><span class="idiff left right"> </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;">"w"</span><span class="p">);</span></span>
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685
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<pre style="margin: 0;">-<span id="LC685" class="line" lang="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;">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 creating 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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686
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<pre style="margin: 0;">-<span id="LC686" class="line" lang="cpp"><span class="idiff left right"> </span><span class="p">}</span></span>
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687
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<pre style="margin: 0;">-<span id="LC687" class="line" lang="cpp"><span class="idiff left right"> </span><span class="p">}</span></span>
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749
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<pre style="margin: 0;">+<span id="LC749" class="line" lang="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">GStr</span> <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="n" style="color: #333;">opt</span><span class="p">);</span></span>
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750
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<pre style="margin: 0;">+<span id="LC750" class="line" lang="cpp"><span class="idiff left right"> </span><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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751
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<pre style="margin: 0;">+<span id="LC751" 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;">s</span><span class="o" style="font-weight: 600;">==</span><span class="sc" style="color: #d14;">'-'</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="cpp"><span class="idiff left right"> </span><span class="n" style="color: #333;">f</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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753
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<pre style="margin: 0;">+<span id="LC753" class="line" lang="cpp"><span class="idiff left right"> </span><span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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754
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<pre style="margin: 0;">+<span id="LC754" class="line" lang="cpp"><span class="idiff left right"> </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;">"w"</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="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;">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 creating 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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756
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<pre style="margin: 0;">+<span id="LC756" 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="LC757" 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="LC758" class="line" lang="cpp"><span class="p">}</span></span>
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689
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759
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<pre style="margin: 0;"> <span id="LC759" class="line" lang="cpp"></span>
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760
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<pre style="margin: 0;"> <span id="LC760" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#define FWCLOSE(fh) if (fh!=NULL && fh!=stdout) fclose(fh)</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">@@ -840,11 +910,104 @@ void printGffObj(FILE* f, GffObj* gfo, GStr& locname, GffPrintMode exonPrinting,</td>
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840
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910
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<pre style="margin: 0;"> <span id="LC910" class="line" lang="cpp"><span class="p">}</span></span>
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841
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911
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<pre style="margin: 0;"> <span id="LC911" class="line" lang="cpp"></span>
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842
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912
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<pre style="margin: 0;"> <span id="LC912" class="line" lang="cpp"></span>
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913
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<pre style="margin: 0;">+<span id="LC913" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">printGxfTab</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">FILE</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">f</span><span class="p">,</span> <span class="n" style="color: #333;">GffObj</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">g</span><span class="p">)</span> <span class="p">{</span></span>
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914
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<pre style="margin: 0;">+<span id="LC914" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//using attribute list in tableCols</span></span>
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915
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<pre style="margin: 0;">+<span id="LC915" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">av</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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916
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<pre style="margin: 0;">+<span id="LC916" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">tableCols</span><span class="p">.</span><span class="n" style="color: #333;">Count</span><span class="p">();</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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917
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<pre style="margin: 0;">+<span id="LC917" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">></span><span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">,</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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918
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<pre style="margin: 0;">+<span id="LC918" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">switch</span><span class="p">(</span><span class="n" style="color: #333;">tableCols</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">type</span><span class="p">)</span> <span class="p">{</span></span>
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919
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<pre style="margin: 0;">+<span id="LC919" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">ctfGFF_Attr</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="920" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
920
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<pre style="margin: 0;">+<span id="LC920" class="line" lang="cpp"> <span class="n" style="color: #333;">av</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">g</span><span class="p">.</span><span class="n" style="color: #333;">getAttr</span><span class="p">(</span><span class="n" style="color: #333;">tableCols</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">name</span><span class="p">.</span><span class="n" style="color: #333;">chars</span><span class="p">());</span></span>
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<td class="diff-line-num new new_line" data-linenumber="921" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
921
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<pre style="margin: 0;">+<span id="LC921" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">av</span><span class="o" style="font-weight: 600;">!=</span><span class="nb" style="color: #0086b3;">NULL</span><span class="p">)</span> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">,</span><span class="s" style="color: #d14;">"%s"</span><span class="p">,</span><span class="n" style="color: #333;">av</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="922" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
922
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<pre style="margin: 0;">+<span id="LC922" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">,</span> <span class="s" style="color: #d14;">"."</span><span class="p">);</span></span>
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923
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<pre style="margin: 0;">+<span id="LC923" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="924" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
924
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<pre style="margin: 0;">+<span id="LC924" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">ctfGFF_chr</span><span class="p">:</span></span>
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925
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<pre style="margin: 0;">+<span id="LC925" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">,</span><span class="s" style="color: #d14;">"%s"</span><span class="p">,</span><span class="n" style="color: #333;">g</span><span class="p">.</span><span class="n" style="color: #333;">getGSeqName</span><span class="p">());</span></span>
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<td class="diff-line-num new new_line" data-linenumber="926" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
926
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<pre style="margin: 0;">+<span id="LC926" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="927" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
927
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<pre style="margin: 0;">+<span id="LC927" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">ctfGFF_ID</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="928" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
928
</td>
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<pre style="margin: 0;">+<span id="LC928" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">,</span><span class="s" style="color: #d14;">"%s"</span><span class="p">,</span><span class="n" style="color: #333;">g</span><span class="p">.</span><span class="n" style="color: #333;">getID</span><span class="p">());</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="843" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="929" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
929
</td>
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<pre style="margin: 0;">+<span id="LC929" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="843" style="width: 35px; color: rgba(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="930" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
930
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<pre style="margin: 0;">+<span id="LC930" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">ctfGFF_Parent</span><span class="p">:</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="843" style="width: 35px; color: rgba(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="931" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
931
</td>
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<pre style="margin: 0;">+<span id="LC931" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">g</span><span class="p">.</span><span class="n" style="color: #333;">parent</span><span class="o" style="font-weight: 600;">!=</span><span class="nb" style="color: #0086b3;">NULL</span><span class="p">)</span> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">,</span><span class="s" style="color: #d14;">"%s"</span><span class="p">,</span><span class="n" style="color: #333;">g</span><span class="p">.</span><span class="n" style="color: #333;">parent</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getID</span><span class="p">());</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="843" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="932" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
932
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC932" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">,</span> <span class="s" style="color: #d14;">"."</span><span class="p">);</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="843" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="933" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
933
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC933" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="843" style="width: 35px; color: rgba(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="934" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
934
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<pre style="margin: 0;">+<span id="LC934" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">ctfGFF_feature</span><span class="p">:</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="843" style="width: 35px; color: rgba(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="935" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
935
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC935" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">,</span><span class="s" style="color: #d14;">"%s"</span><span class="p">,</span><span class="n" style="color: #333;">g</span><span class="p">.</span><span class="n" style="color: #333;">getFeatureName</span><span class="p">());</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="843" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="936" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
936
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC936" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
</pre>
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</td>
<td class="diff-line-num new new_line" data-linenumber="937" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
937
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<pre style="margin: 0;">+<span id="LC937" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">ctfGFF_start</span><span class="p">:</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="843" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="938" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
938
</td>
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<pre style="margin: 0;">+<span id="LC938" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">,</span><span class="s" style="color: #d14;">"%d"</span><span class="p">,</span><span class="n" style="color: #333;">g</span><span class="p">.</span><span class="n" style="color: #333;">start</span><span class="p">);</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="843" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="939" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
939
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC939" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="843" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="940" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
940
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<pre style="margin: 0;">+<span id="LC940" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">ctfGFF_end</span><span class="p">:</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="843" style="width: 35px; color: rgba(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="941" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
941
</td>
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<pre style="margin: 0;">+<span id="LC941" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">,</span><span class="s" style="color: #d14;">"%d"</span><span class="p">,</span><span class="n" style="color: #333;">g</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">);</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="843" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="942" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
942
</td>
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<pre style="margin: 0;">+<span id="LC942" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="843" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="943" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
943
</td>
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<pre style="margin: 0;">+<span id="LC943" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">ctfGFF_strand</span><span class="p">:</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="843" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="944" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
944
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC944" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">,</span><span class="s" style="color: #d14;">"%c"</span><span class="p">,</span><span class="n" style="color: #333;">g</span><span class="p">.</span><span class="n" style="color: #333;">strand</span><span class="p">);</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="843" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="945" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
945
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC945" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="843" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="946" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
946
</td>
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<pre style="margin: 0;">+<span id="LC946" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">ctfGFF_numexons</span><span class="p">:</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="843" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="947" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
947
</td>
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<pre style="margin: 0;">+<span id="LC947" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">,</span><span class="s" style="color: #d14;">"%d"</span><span class="p">,</span><span class="n" style="color: #333;">g</span><span class="p">.</span><span class="n" style="color: #333;">exons</span><span class="p">.</span><span class="n" style="color: #333;">Count</span><span class="p">());</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="843" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="948" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
948
</td>
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<pre style="margin: 0;">+<span id="LC948" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
</pre>
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949
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<pre style="margin: 0;">+<span id="LC949" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">ctfGFF_exons</span><span class="p">:</span></span>
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950
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<pre style="margin: 0;">+<span id="LC950" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">g</span><span class="p">.</span><span class="n" style="color: #333;">exons</span><span class="p">.</span><span class="n" style="color: #333;">Count</span><span class="p">()</span><span class="o" style="font-weight: 600;">></span><span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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951
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<pre style="margin: 0;">+<span id="LC951" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span><span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">g</span><span class="p">.</span><span class="n" style="color: #333;">exons</span><span class="p">.</span><span class="n" style="color: #333;">Count</span><span class="p">();</span><span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="952" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
952
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<pre style="margin: 0;">+<span id="LC952" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">></span><span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">,</span><span class="s" style="color: #d14;">","</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="953" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
953
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<pre style="margin: 0;">+<span id="LC953" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">,</span><span class="s" style="color: #d14;">"%d-%d"</span><span class="p">,</span><span class="n" style="color: #333;">g</span><span class="p">.</span><span class="n" style="color: #333;">exons</span><span class="p">[</span><span class="n" style="color: #333;">x</span><span class="p">]</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="n" style="color: #333;">g</span><span class="p">.</span><span class="n" style="color: #333;">exons</span><span class="p">[</span><span class="n" style="color: #333;">x</span><span class="p">]</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">end</span><span class="p">);</span></span>
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954
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<pre style="margin: 0;">+<span id="LC954" class="line" lang="cpp"> <span class="p">}</span></span>
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955
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<pre style="margin: 0;">+<span id="LC955" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">,</span><span class="s" style="color: #d14;">"."</span><span class="p">);</span></span>
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956
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<pre style="margin: 0;">+<span id="LC956" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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957
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<pre style="margin: 0;">+<span id="LC957" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">ctfGFF_cds</span><span class="p">:</span></span>
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958
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<pre style="margin: 0;">+<span id="LC958" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">g</span><span class="p">.</span><span class="n" style="color: #333;">hasCDS</span><span class="p">())</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="959" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
959
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<pre style="margin: 0;">+<span id="LC959" class="line" lang="cpp"> <span class="n" style="color: #333;">GVec</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">GffExon</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">cds</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="960" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
960
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<pre style="margin: 0;">+<span id="LC960" class="line" lang="cpp"> <span class="n" style="color: #333;">g</span><span class="p">.</span><span class="n" style="color: #333;">getCDSegs</span><span class="p">(</span><span class="n" style="color: #333;">cds</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="961" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
961
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<pre style="margin: 0;">+<span id="LC961" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span><span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">cds</span><span class="p">.</span><span class="n" style="color: #333;">Count</span><span class="p">();</span><span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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962
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<pre style="margin: 0;">+<span id="LC962" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">></span><span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">,</span><span class="s" style="color: #d14;">","</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="963" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
963
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<pre style="margin: 0;">+<span id="LC963" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">,</span><span class="s" style="color: #d14;">"%d-%d"</span><span class="p">,</span><span class="n" style="color: #333;">cds</span><span class="p">[</span><span class="n" style="color: #333;">x</span><span class="p">].</span><span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="n" style="color: #333;">cds</span><span class="p">[</span><span class="n" style="color: #333;">x</span><span class="p">].</span><span class="n" style="color: #333;">end</span><span class="p">);</span></span>
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964
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<pre style="margin: 0;">+<span id="LC964" class="line" lang="cpp"> <span class="p">}</span></span>
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965
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<pre style="margin: 0;">+<span id="LC965" class="line" lang="cpp"> <span class="p">}</span></span>
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966
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<pre style="margin: 0;">+<span id="LC966" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">,</span><span class="s" style="color: #d14;">"."</span><span class="p">);</span></span>
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967
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<pre style="margin: 0;">+<span id="LC967" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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968
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<pre style="margin: 0;">+<span id="LC968" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">ctfGFF_covlen</span><span class="p">:</span></span>
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969
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<pre style="margin: 0;">+<span id="LC969" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">,</span> <span class="s" style="color: #d14;">"%d"</span><span class="p">,</span> <span class="n" style="color: #333;">g</span><span class="p">.</span><span class="n" style="color: #333;">covlen</span><span class="p">);</span></span>
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970
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<pre style="margin: 0;">+<span id="LC970" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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971
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<pre style="margin: 0;">+<span id="LC971" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">ctfGFF_cdslen</span><span class="p">:</span></span>
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972
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<pre style="margin: 0;">+<span id="LC972" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">g</span><span class="p">.</span><span class="n" style="color: #333;">hasCDS</span><span class="p">())</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="973" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
973
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<pre style="margin: 0;">+<span id="LC973" class="line" lang="cpp"> <span class="n" style="color: #333;">GVec</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">GffExon</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">cds</span><span class="p">;</span></span>
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974
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<pre style="margin: 0;">+<span id="LC974" class="line" lang="cpp"> <span class="n" style="color: #333;">g</span><span class="p">.</span><span class="n" style="color: #333;">getCDSegs</span><span class="p">(</span><span class="n" style="color: #333;">cds</span><span class="p">);</span></span>
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975
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<pre style="margin: 0;">+<span id="LC975" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">clen</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="976" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
976
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<pre style="margin: 0;">+<span id="LC976" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span><span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">cds</span><span class="p">.</span><span class="n" style="color: #333;">Count</span><span class="p">();</span><span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>
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977
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<pre style="margin: 0;">+<span id="LC977" class="line" lang="cpp"> <span class="n" style="color: #333;">clen</span><span class="o" style="font-weight: 600;">+=</span><span class="n" style="color: #333;">cds</span><span class="p">[</span><span class="n" style="color: #333;">x</span><span class="p">].</span><span class="n" style="color: #333;">end</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">cds</span><span class="p">[</span><span class="n" style="color: #333;">x</span><span class="p">].</span><span class="n" style="color: #333;">start</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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978
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<pre style="margin: 0;">+<span id="LC978" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">,</span> <span class="s" style="color: #d14;">"%d"</span><span class="p">,</span> <span class="n" style="color: #333;">clen</span><span class="p">);</span></span>
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979
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<pre style="margin: 0;">+<span id="LC979" class="line" lang="cpp"> <span class="p">}</span></span>
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980
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<pre style="margin: 0;">+<span id="LC980" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">,</span> <span class="s" style="color: #d14;">"0"</span><span class="p">);</span></span>
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981
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<pre style="margin: 0;">+<span id="LC981" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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982
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<pre style="margin: 0;">+<span id="LC982" class="line" lang="cpp"> <span class="p">}</span></span>
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983
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<pre style="margin: 0;">+<span id="LC983" class="line" lang="cpp"> <span class="p">}</span></span>
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984
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<pre style="margin: 0;">+<span id="LC984" 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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985
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<pre style="margin: 0;">+<span id="LC985" class="line" lang="cpp"><span class="p">}</span></span>
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986
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<pre style="margin: 0;">+<span id="LC986" class="line" lang="cpp"></span>
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987
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<pre style="margin: 0;">+<span id="LC987" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">printAsTable</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">FILE</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">f</span><span class="p">,</span> <span class="n" style="color: #333;">GffObj</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">gfo</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">out_counter</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">NULL</span><span class="p">)</span> <span class="p">{</span></span>
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988
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<pre style="margin: 0;">+<span id="LC988" class="line" lang="cpp"> <span class="n" style="color: #333;">GffObj</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">t</span><span class="o" style="font-weight: 600;">=*</span><span class="n" style="color: #333;">gfo</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="989" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
989
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<pre style="margin: 0;">+<span id="LC989" class="line" lang="cpp"> <span class="n" style="color: #333;">GTData</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">tdata</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="n" style="color: #333;">GTData</span><span class="o" style="font-weight: 600;">*</span><span class="p">)(</span><span class="n" style="color: #333;">t</span><span class="p">.</span><span class="n" style="color: #333;">uptr</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="990" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
990
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<pre style="margin: 0;">+<span id="LC990" 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="o" style="font-weight: 600;">||</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="k" style="font-weight: 600;">return</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="991" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
991
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<pre style="margin: 0;">+<span id="LC991" 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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992
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<pre style="margin: 0;">+<span id="LC992" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">out_counter</span><span class="o" style="font-weight: 600;">!=</span><span class="nb" style="color: #0086b3;">NULL</span><span class="p">)</span> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">out_counter</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 new new_line" data-linenumber="993" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
993
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<pre style="margin: 0;">+<span id="LC993" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//print the parent first, if any and if not printed already</span></span>
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<td class="diff-line-num new new_line" data-linenumber="994" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
994
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<pre style="margin: 0;">+<span id="LC994" 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;">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;">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;">parent</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">udata</span><span class="p">))</span> <span class="p">{</span></span>
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995
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<pre style="margin: 0;">+<span id="LC995" 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;">pdata</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;">parent</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">uptr</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="996" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
996
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<pre style="margin: 0;">+<span id="LC996" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">pdata</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">pdata</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">geneinfo</span><span class="o" style="font-weight: 600;">!=</span><span class="nb" style="color: #0086b3;">NULL</span><span class="p">)</span></span>
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997
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<pre style="margin: 0;">+<span id="LC997" class="line" lang="cpp"> <span class="n" style="color: #333;">pdata</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">geneinfo</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">finalize</span><span class="p">();</span></span>
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998
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<pre style="margin: 0;">+<span id="LC998" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//t.parent->addAttr("locus", locname.chars());</span></span>
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999
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<pre style="margin: 0;">+<span id="LC999" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//(*out_counter)++; ?</span></span>
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1000
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<pre style="margin: 0;">+<span id="LC1000" class="line" lang="cpp"> <span class="n" style="color: #333;">printGxfTab</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">t</span><span class="p">.</span><span class="n" style="color: #333;">parent</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1001" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1001
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<pre style="margin: 0;">+<span id="LC1001" class="line" lang="cpp"> <span class="n" style="color: #333;">T_NO_PRINT</span><span class="p">(</span><span class="n" style="color: #333;">t</span><span class="p">.</span><span class="n" style="color: #333;">parent</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">udata</span><span class="p">);</span></span>
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1002
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<pre style="margin: 0;">+<span id="LC1002" class="line" lang="cpp"> <span class="p">}</span></span>
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1003
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<pre style="margin: 0;">+<span id="LC1003" class="line" lang="cpp"> <span class="n" style="color: #333;">printGxfTab</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">gfo</span><span class="p">);</span></span>
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1004
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<pre style="margin: 0;">+<span id="LC1004" class="line" lang="cpp"><span class="p">}</span></span>
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1005
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<pre style="margin: 0;">+<span id="LC1005" class="line" lang="cpp"></span>
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843
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1006
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<pre style="margin: 0;"> <span id="LC1006" 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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844
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<td class="diff-line-num new_line" data-linenumber="1007" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1007
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<pre style="margin: 0;"> <span id="LC1007" 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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845
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1008
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<pre style="margin: 0;"> <span id="LC1008" class="line" lang="cpp"> <span class="s" style="color: #d14;">"version;debug;merge;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="LC846" class="line" lang="cpp"> <span class="s" style="color: #d14;">"sort-alpha;keep-genes;keep-comments;keep-exon-attrs;force-exons;gene2exon;"</span></span>
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<td class="diff-line-num old old_line" data-linenumber="847" 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">
847
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<pre style="margin: 0;">-<span id="LC847" class="line" lang="cpp"> <span class="s" style="color: #d14;">"ignore-locus;no-pseudo;sort-by=hvOUNHPWCVJMKQYTDARSZFGLEBm:g:i:r:s:l:t:o:w:x:y:d:"</span><span class="p">);</span></span>
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<td class="diff-line-num new old_line" data-linenumber="848" style="width: 35px; color: rgba(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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1009
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<pre style="margin: 0;">+<span id="LC1009" class="line" lang="cpp"> <span class="s" style="color: #d14;">"sort-alpha;keep-genes;keep-comments;keep-exon-attrs;force-exons;<span class="idiff left right">t-adopt;</span>gene2exon;"</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1010" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1010
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<pre style="margin: 0;">+<span id="LC1010" class="line" lang="cpp"> <span class="s" style="color: #d14;">"ignore-locus;no-pseudo;<span class="idiff left right">table=</span>sort-by=hvOUNHPWCVJMKQYTDARSZFGLEBm:g:i:r:s:l:t:o:w:x:y:d:"</span><span class="p">);</span></span>
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848
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<td class="diff-line-num new_line" data-linenumber="1011" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1011
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<pre style="margin: 0;"> <span id="LC1011" 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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849
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1012
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<pre style="margin: 0;"> <span id="LC1012" 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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850
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1013
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<pre style="margin: 0;"> <span id="LC1013" class="line" lang="cpp"> <span class="n" style="color: #333;">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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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="887" style="width: 35px; color: rgba(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="1050" style="width: 35px; color: rgba(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">@@ -887,6 +1050,7 @@ int main(int argc, char* argv[]) {</td>
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887
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1050
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<pre style="margin: 0;"> <span id="LC1050" class="line" lang="cpp"> <span class="n" style="color: #333;">StarStop</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;">'S'</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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888
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<td class="diff-line-num new_line" data-linenumber="1051" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1051
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<pre style="margin: 0;"> <span id="LC1051" class="line" lang="cpp"></span>
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<td class="diff-line-num old_line" data-linenumber="889" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
889
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<td class="diff-line-num new_line" data-linenumber="1052" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1052
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<pre style="margin: 0;"> <span id="LC1052" class="line" lang="cpp"> <span class="n" style="color: #333;">gffloader</span><span class="p">.</span><span class="n" style="color: #333;">keepGenes</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;">"keep-genes"</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 new new_line" data-linenumber="1053" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1053
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<pre style="margin: 0;">+<span id="LC1053" class="line" lang="cpp"> <span class="n" style="color: #333;">gffloader</span><span class="p">.</span><span class="n" style="color: #333;">trAdoption</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;">"t-adopt"</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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890
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<td class="diff-line-num new_line" data-linenumber="1054" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1054
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<pre style="margin: 0;"> <span id="LC1054" class="line" lang="cpp"> <span class="n" style="color: #333;">gffloader</span><span class="p">.</span><span class="n" style="color: #333;">keepGff3Comments</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;">"keep-comments"</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 old_line" data-linenumber="891" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
891
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<td class="diff-line-num new_line" data-linenumber="1055" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1055
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<pre style="margin: 0;"> <span id="LC1055" class="line" lang="cpp"> <span class="n" style="color: #333;">gffloader</span><span class="p">.</span><span class="n" style="color: #333;">sortRefsAlpha</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;">"sort-alpha"</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 old_line" data-linenumber="892" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
892
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<td class="diff-line-num new_line" data-linenumber="1056" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1056
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<pre style="margin: 0;"> <span id="LC1056" 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;">"sort-by"</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 unfold js-unfold old_line" data-linenumber="896" style="width: 35px; color: rgba(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="1060" style="width: 35px; color: rgba(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">@@ -896,7 +1060,6 @@ int main(int argc, char* argv[]) {</td>
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896
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1060
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<pre style="margin: 0;"> <span id="LC1060" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="897" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
897
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<td class="diff-line-num new_line" data-linenumber="1061" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1061
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<pre style="margin: 0;"> <span id="LC1061" 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;">sortBy</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 old_line" data-linenumber="898" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
898
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<td class="diff-line-num new_line" data-linenumber="1062" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1062
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<pre style="margin: 0;"> <span id="LC1062" class="line" lang="cpp"> <span class="n" style="color: #333;">gffloader</span><span class="p">.</span><span class="n" style="color: #333;">loadRefNames</span><span class="p">(</span><span class="n" style="color: #333;">sortBy</span><span class="p">);</span></span>
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899
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<pre style="margin: 0;">-<span id="LC899" class="line" lang="cpp"></span>
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900
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1063
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<pre style="margin: 0;"> <span id="LC1063" class="line" lang="cpp"> <span class="n" style="color: #333;">gffloader</span><span class="p">.</span><span class="n" style="color: #333;">gene2exon</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;">"gene2exon"</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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901
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1064
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<pre style="margin: 0;"> <span id="LC1064" class="line" lang="cpp"> <span class="n" style="color: #333;">gffloader</span><span class="p">.</span><span class="n" style="color: #333;">matchAllIntrons</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;">'K'</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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902
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<td class="diff-line-num new_line" data-linenumber="1065" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1065
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<pre style="margin: 0;"> <span id="LC1065" class="line" lang="cpp"> <span class="n" style="color: #333;">gffloader</span><span class="p">.</span><span class="n" style="color: #333;">fuzzSpan</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;">'Q'</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="956" style="width: 35px; color: rgba(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="1119" style="width: 35px; color: rgba(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">@@ -956,6 +1119,14 @@ int main(int argc, char* argv[]) {</td>
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956
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<td class="diff-line-num new_line" data-linenumber="1119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1119
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<pre style="margin: 0;"> <span id="LC1119" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//sortByLoc=true;</span></span>
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957
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1120
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<pre style="margin: 0;"> <span id="LC1120" class="line" lang="cpp"> <span class="p">}</span></span>
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958
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<td class="diff-line-num new_line" data-linenumber="1121" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1121
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<pre style="margin: 0;"> <span id="LC1121" class="line" lang="cpp"></span>
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1122
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<pre style="margin: 0;">+<span id="LC1122" class="line" lang="cpp"> <span class="n" style="color: #333;">tableFormat</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;">"table"</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1123" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1123
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<pre style="margin: 0;">+<span id="LC1123" 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;">tableFormat</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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1124
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<pre style="margin: 0;">+<span id="LC1124" class="line" lang="cpp"> <span class="n" style="color: #333;">setTableFormat</span><span class="p">(</span><span class="n" style="color: #333;">tableFormat</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1125" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1125
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<pre style="margin: 0;">+<span id="LC1125" class="line" lang="cpp"> <span class="n" style="color: #333;">fmtTable</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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<td class="diff-line-num new new_line" data-linenumber="1126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1126
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<pre style="margin: 0;">+<span id="LC1126" class="line" lang="cpp"> <span class="n" style="color: #333;">fmtGFF3</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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1127
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<pre style="margin: 0;">+<span id="LC1127" 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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<td class="diff-line-num new new_line" data-linenumber="1128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1128
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<pre style="margin: 0;">+<span id="LC1128" class="line" lang="cpp"> <span class="p">}</span></span>
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1129
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<pre style="margin: 0;">+<span id="LC1129" class="line" lang="cpp"></span>
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959
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1130
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<pre style="margin: 0;"> <span id="LC1130" class="line" lang="cpp"> <span class="n" style="color: #333;">gffloader</span><span class="p">.</span><span class="n" style="color: #333;">mergeCloseExons</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;">'Z'</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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960
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1131
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<pre style="margin: 0;"> <span id="LC1131" class="line" lang="cpp"> <span class="n" style="color: #333;">multiExon</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;">'U'</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 old_line" data-linenumber="961" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
961
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<td class="diff-line-num new_line" data-linenumber="1132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1132
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<pre style="margin: 0;"> <span id="LC1132" class="line" lang="cpp"> <span class="n" style="color: #333;">writeExonSegs</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;">'W'</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="1040" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1211" style="width: 35px; color: rgba(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">@@ -1040,6 +1211,9 @@ int main(int argc, char* argv[]) {</td>
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1040
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1211
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<pre style="margin: 0;"> <span id="LC1211" 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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<td class="diff-line-num old_line" data-linenumber="1041" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1041
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<td class="diff-line-num new_line" data-linenumber="1212" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1212
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<pre style="margin: 0;"> <span id="LC1212" 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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<td class="diff-line-num old_line" data-linenumber="1042" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1042
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<td class="diff-line-num new_line" data-linenumber="1213" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1213
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<pre style="margin: 0;"> <span id="LC1213" 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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1214
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<pre style="margin: 0;">+<span id="LC1214" class="line" lang="cpp"></span>
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1215
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<pre style="margin: 0;">+<span id="LC1215" 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="p">)</span></span>
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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;">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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1043
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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;">//if (f_y!=NULL || f_x!=NULL) wCDSonly=true;</span></span>
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1044
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<td class="diff-line-num new_line" data-linenumber="1218" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1218
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<pre style="margin: 0;"> <span id="LC1218" 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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1045
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1219
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<pre style="margin: 0;"> <span id="LC1219" class="line" lang="cpp"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1180" style="width: 35px; color: rgba(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="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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1180,7 +1354,8 @@ int main(int argc, char* argv[]) {</td>
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1180
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1354
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<pre style="margin: 0;"> <span id="LC1354" 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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1181
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1355
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<pre style="margin: 0;"> <span id="LC1355" class="line" lang="cpp"> <span class="p">}</span></span>
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1182
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1356
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<pre style="margin: 0;"> <span id="LC1356" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1183" 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">
1183
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<pre style="margin: 0;">-<span id="LC1183" 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;">rnas</span><span class="p">[</span><span class="n" style="color: #333;">rnas_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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1357
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<pre style="margin: 0;">+<span id="LC1357" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">fmtTable</span><span class="p">)</span> <span class="n" style="color: #333;">printAsTable</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;">rnas</span><span class="p">[</span><span class="n" style="color: #333;">rnas_i</span><span class="p">],</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">out_counter</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1358" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1358
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<pre style="margin: 0;">+<span id="LC1358" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <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;">rnas</span><span class="p">[</span><span class="n" style="color: #333;">rnas_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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1184
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1359
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<pre style="margin: 0;"> <span id="LC1359" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">rnas_i</span><span class="p">;</span></span>
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1185
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1360
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<pre style="margin: 0;"> <span id="LC1360" class="line" lang="cpp"> <span class="p">}</span></span>
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1186
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1361
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<pre style="margin: 0;"> <span id="LC1361" 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="1197" style="width: 35px; color: rgba(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="1372" style="width: 35px; color: rgba(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">@@ -1197,18 +1372,21 @@ int main(int argc, char* argv[]) {</td>
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1197
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1372
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<pre style="margin: 0;"> <span id="LC1372" 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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<td class="diff-line-num old_line" data-linenumber="1198" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1198
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<td class="diff-line-num new_line" data-linenumber="1373" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1373
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<pre style="margin: 0;"> <span id="LC1373" 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;">m</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;">m</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;">rnas</span><span class="p">.</span><span class="n" style="color: #333;">Count</span><span class="p">();</span><span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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1199
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<td class="diff-line-num new_line" data-linenumber="1374" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1374
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<pre style="margin: 0;"> <span id="LC1374" 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;">gdata</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">rnas</span><span class="p">[</span><span class="n" style="color: #333;">m</span><span class="p">]);</span></span>
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1200
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<pre style="margin: 0;">-<span id="LC1200" 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;"><span class="idiff left right">fmtGFF3</span></span><span class="p">)</span> <span class="p">{</span></span>
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1375
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<pre style="margin: 0;">+<span id="LC1375" 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 class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">fmtGFF3</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">||</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">fmtTable</span></span><span class="p"><span class="idiff right">)</span>)</span> <span class="p">{</span></span>
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1201
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<td class="diff-line-num new_line" data-linenumber="1376" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1376
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<pre style="margin: 0;"> <span id="LC1376" 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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<td class="diff-line-num old old_line" data-linenumber="1202" 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">
1202
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<td class="diff-line-num new_line old" data-linenumber="1377" 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="LC1202" 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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1203
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<td class="diff-line-num new_line old" data-linenumber="1377" 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="LC1203" 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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1204
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<td class="diff-line-num new_line old" data-linenumber="1377" 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="LC1204" 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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<td class="diff-line-num old old_line" data-linenumber="1205" 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">
1205
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<td class="diff-line-num new_line old" data-linenumber="1377" 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="LC1205" 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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<td class="diff-line-num old old_line" data-linenumber="1206" 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">
1206
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<td class="diff-line-num new_line old" data-linenumber="1377" 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="LC1206" 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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1207
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<td class="diff-line-num new_line old" data-linenumber="1377" 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="LC1207" 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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1208
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<pre style="margin: 0;">-<span id="LC1208" class="line" lang="cpp"> <span class="n" style="color: #333;">gfst</span><span class="p">.</span><span class="n" style="color: #333;">printGxf</span><span class="p">(</span><span class="n" style="color: #333;">f_out</span><span class="p">,</span> <span class="n" style="color: #333;">exonPrinting</span><span class="p">,</span> <span class="n" style="color: #333;">tracklabel</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="n" style="color: #333;">decodeChars</span><span class="p">);</span></span>
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1209
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<td class="diff-line-num new_line old" data-linenumber="1377" 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="LC1209" class="line" lang="cpp"> <span class="p">}</span></span>
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1210
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<td class="diff-line-num new_line old" data-linenumber="1377" 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="LC1210" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">gfs_i</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1211" 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">
1211
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<td class="diff-line-num new_line old" data-linenumber="1377" 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="LC1211" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1212" style="width: 35px; color: rgba(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="1377" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1377
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<pre style="margin: 0;">+<span id="LC1377" 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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<td class="diff-line-num new new_line" data-linenumber="1378" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1378
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<pre style="margin: 0;">+<span id="LC1378" 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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<td class="diff-line-num new new_line" data-linenumber="1379" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1379
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<pre style="margin: 0;">+<span id="LC1379" 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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<td class="diff-line-num new new_line" data-linenumber="1380" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1380
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<pre style="margin: 0;">+<span id="LC1380" 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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<td class="diff-line-num new new_line" data-linenumber="1381" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1381
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<pre style="margin: 0;">+<span id="LC1381" 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 new new_line" data-linenumber="1382" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1382
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<pre style="margin: 0;">+<span id="LC1382" 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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<td class="diff-line-num new new_line" data-linenumber="1383" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1383
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<pre style="margin: 0;">+<span id="LC1383" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">firstGSeqHeader</span><span class="p">)</span> <span class="p">{</span> <span class="n" style="color: #333;">printGSeqHeader</span><span class="p">(</span><span class="n" style="color: #333;">f_out</span><span class="p">,</span> <span class="n" style="color: #333;">gdata</span><span class="p">);</span> <span class="n" style="color: #333;">firstGSeqHeader</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">false</span><span class="p">;</span> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1384" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1384
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<pre style="margin: 0;">+<span id="LC1384" class="line" lang="cpp"> <span class="n" style="color: #333;">gfst</span><span class="p">.</span><span class="n" style="color: #333;">printGxf</span><span class="p">(</span><span class="n" style="color: #333;">f_out</span><span class="p">,</span> <span class="n" style="color: #333;">exonPrinting</span><span class="p">,</span> <span class="n" style="color: #333;">tracklabel</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="n" style="color: #333;">decodeChars</span><span class="p">);</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1212" style="width: 35px; color: rgba(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="1385" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1385
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<pre style="margin: 0;">+<span id="LC1385" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1212" style="width: 35px; color: rgba(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="1386" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1386
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<pre style="margin: 0;">+<span id="LC1386" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">printGxfTab</span><span class="p">(</span><span class="n" style="color: #333;">f_out</span><span class="p">,</span> <span class="n" style="color: #333;">gfst</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1387" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1387
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<pre style="margin: 0;">+<span id="LC1387" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1212" style="width: 35px; color: rgba(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="1388" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1388
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<pre style="margin: 0;">+<span id="LC1388" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">gfs_i</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1389" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1389
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<pre style="margin: 0;">+<span id="LC1389" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="1212" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1212
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<td class="diff-line-num 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">
1390
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<pre style="margin: 0;"> <span id="LC1390" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="1213" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1213
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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;">GTData</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">tdata</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="n" style="color: #333;">GTData</span><span class="o" style="font-weight: 600;">*</span><span class="p">)(</span><span class="n" style="color: #333;">t</span><span class="p">.</span><span class="n" style="color: #333;">uptr</span><span class="p">);</span></span>
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<td class="diff-line-num old_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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<td class="diff-line-num new_line" data-linenumber="1392" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1392
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<pre style="margin: 0;"> <span id="LC1392" 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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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1216" style="width: 35px; color: rgba(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="1394" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1216,36 +1394,46 @@ int main(int argc, char* argv[]) {</td>
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1216
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<td class="diff-line-num new_line" data-linenumber="1394" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1394
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<pre style="margin: 0;"> <span id="LC1394" 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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<td class="diff-line-num old_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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<td class="diff-line-num new_line" data-linenumber="1395" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1395
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<pre style="margin: 0;"> <span id="LC1395" 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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<td class="diff-line-num old_line" data-linenumber="1218" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1218
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<td class="diff-line-num new_line" data-linenumber="1396" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1396
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<pre style="margin: 0;"> <span id="LC1396" 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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<td class="diff-line-num old old_line" data-linenumber="1219" 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">
1219
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<td class="diff-line-num new_line old" data-linenumber="1397" 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="LC1219" 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;">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 new old_line" data-linenumber="1220" style="width: 35px; color: rgba(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="1397" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1397
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<pre style="margin: 0;">+<span id="LC1397" 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;"><span class="idiff left">fmtTable</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;">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 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">
1220
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<td class="diff-line-num new_line" data-linenumber="1398" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1398
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<pre style="margin: 0;"> <span id="LC1398" 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;">geneinfo</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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<td class="diff-line-num new_line" data-linenumber="1399" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1399
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<pre style="margin: 0;"> <span id="LC1399" class="line" lang="cpp"> <span class="n" style="color: #333;">tdata</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">geneinfo</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">finalize</span><span class="p">();</span></span>
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<td class="diff-line-num old_line" data-linenumber="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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<td class="diff-line-num 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">
1400
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<pre style="margin: 0;"> <span id="LC1400" class="line" lang="cpp"> <span class="n" style="color: #333;">out_counter</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="1401" 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="c1" style="color: #998; font-style: italic;">// if (fmtGTF) t.printGxf(f_out, exonPrinting, tracklabel, NULL, decodeChars);</span></span>
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1224
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<pre style="margin: 0;">-<span id="LC1224" 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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1225
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<pre style="margin: 0;">-<span id="LC1225" 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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1226
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<td class="diff-line-num new_line old" data-linenumber="1401" 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="LC1226" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//for GFF3, print the parent first, if any</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1227" 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">
1227
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<td class="diff-line-num new_line old" data-linenumber="1401" 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="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;">t</span><span class="p">.</span><span class="n" style="color: #333;">parent</span><span class="o" style="font-weight: 600;">!=</span><span class="nb" style="color: #0086b3;">NULL</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">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;">parent</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">udata</span><span class="p">))</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1401" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1401
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<pre style="margin: 0;">+<span id="LC1401" 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 new new_line" data-linenumber="1402" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1402
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<pre style="margin: 0;">+<span id="LC1402" 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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<td class="diff-line-num new new_line" data-linenumber="1403" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1403
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<pre style="margin: 0;">+<span id="LC1403" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">firstGSeqHeader</span><span class="p">)</span> <span class="p">{</span> <span class="n" style="color: #333;">printGSeqHeader</span><span class="p">(</span><span class="n" style="color: #333;">f_out</span><span class="p">,</span> <span class="n" style="color: #333;">gdata</span><span class="p">);</span> <span class="n" style="color: #333;">firstGSeqHeader</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">false</span><span class="p">;</span> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1404" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1404
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<pre style="margin: 0;">+<span id="LC1404" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1405" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1405
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<pre style="margin: 0;">+<span id="LC1405" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//for GFF3 && table output, print the parent first, if any</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1406" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1406
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<pre style="margin: 0;">+<span id="LC1406" 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="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">t</span><span class="p">.</span><span class="n" style="color: #333;">parent</span><span class="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_PRINTABLE</span><span class="p">(</span><span class="n" style="color: #333;">t</span><span class="p">.</span><span class="n" style="color: #333;">parent</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">udata</span><span class="p">))</span> <span class="p">{</span></span>
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1228
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<td class="diff-line-num new_line" data-linenumber="1407" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1407
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<pre style="margin: 0;"> <span id="LC1407" 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;">pdata</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;">parent</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">uptr</span><span class="p">);</span></span>
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1229
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<td class="diff-line-num new_line" data-linenumber="1408" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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;">pdata</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">pdata</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">geneinfo</span><span class="o" style="font-weight: 600;">!=</span><span class="nb" style="color: #0086b3;">NULL</span><span class="p">)</span></span>
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<td class="diff-line-num old_line" data-linenumber="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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<td class="diff-line-num new_line" data-linenumber="1409" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1409
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<pre style="margin: 0;"> <span id="LC1409" class="line" lang="cpp"> <span class="n" style="color: #333;">pdata</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">geneinfo</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">finalize</span><span class="p">();</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1231" 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">
1231
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<td class="diff-line-num new_line old" data-linenumber="1410" 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="LC1231" class="line" lang="cpp"> <span class="n" style="color: #333;">t</span><span class="p">.</span><span class="n" style="color: #333;">parent</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">printGxf</span><span class="p">(</span><span class="n" style="color: #333;">f_out</span><span class="p">,</span> <span class="n" style="color: #333;">exonPrinting</span><span class="p">,</span> <span class="n" style="color: #333;">tracklabel</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="n" style="color: #333;">decodeChars</span><span class="p">);</span></span>
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1410
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<pre style="margin: 0;">+<span id="LC1410" 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 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="n" style="color: #333;">printGxfTab</span><span class="p">(</span><span class="n" style="color: #333;">f_out</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">t</span><span class="p">.</span><span class="n" style="color: #333;">parent</span><span class="p">));</span></span>
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<td class="diff-line-num new 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="k" style="font-weight: 600;">else</span></span>
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1413
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<pre style="margin: 0;">+<span id="LC1413" class="line" lang="cpp"> <span class="n" style="color: #333;">t</span><span class="p">.</span><span class="n" style="color: #333;">parent</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">printGxf</span><span class="p">(</span><span class="n" style="color: #333;">f_out</span><span class="p">,</span> <span class="n" style="color: #333;">exonPrinting</span><span class="p">,</span> <span class="n" style="color: #333;">tracklabel</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="n" style="color: #333;">decodeChars</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="1232" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1232
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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="n" style="color: #333;">T_NO_PRINT</span><span class="p">(</span><span class="n" style="color: #333;">t</span><span class="p">.</span><span class="n" style="color: #333;">parent</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">udata</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="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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<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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1234
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<td class="diff-line-num new_line old" data-linenumber="1416" 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="LC1234" 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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<td class="diff-line-num new old_line" data-linenumber="1235" style="width: 35px; color: rgba(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;">fmtTable</span><span class="p">)</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1235" style="width: 35px; color: rgba(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;">printGxfTab</span><span class="p">(</span><span class="n" style="color: #333;">f_out</span><span class="p">,</span> <span class="n" style="color: #333;">t</span><span class="p">);</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1235" style="width: 35px; color: rgba(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="k" style="font-weight: 600;">else</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1235" style="width: 35px; color: rgba(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="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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<td class="diff-line-num old_line" data-linenumber="1235" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1235
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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="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="1236" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1236
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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="p">}</span><span class="c1" style="color: #998; font-style: italic;">//GFF/GTF output requested</span></span>
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<td class="diff-line-num old_line" data-linenumber="1237" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1237
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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 class="c1" style="color: #998; font-style: italic;">//valid transcript</span></span>
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<td class="diff-line-num old_line" data-linenumber="1238" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1238
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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 class="p">}</span> <span class="c1" style="color: #998; font-style: italic;">//for each rna</span></span>
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<td class="diff-line-num old_line" data-linenumber="1239" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1239
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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="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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<td class="diff-line-num old old_line" data-linenumber="1240" 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">
1240
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<td class="diff-line-num new_line old" data-linenumber="1425" 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="LC1240" 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;"><span class="idiff left right">fmtGFF3</span></span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1241" style="width: 35px; color: rgba(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="1425" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1425
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<pre style="margin: 0;">+<span id="LC1425" 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 class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">fmtGFF3</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">||</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">fmtTable</span></span><span class="p"><span class="idiff right">)</span>)</span> <span class="p">{</span></span>
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1241
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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="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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<td class="diff-line-num old_line" data-linenumber="1242" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1242
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<td class="diff-line-num new_line" data-linenumber="1427" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1427
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<pre style="margin: 0;"> <span id="LC1427" 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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<td class="diff-line-num old_line" data-linenumber="1243" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1243
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<td class="diff-line-num new_line" data-linenumber="1428" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1428
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<pre style="margin: 0;"> <span id="LC1428" 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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<td class="diff-line-num old_line" data-linenumber="1244" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1244
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<td class="diff-line-num new_line" data-linenumber="1429" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1429
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<pre style="margin: 0;"> <span id="LC1429" 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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<td class="diff-line-num old old_line" data-linenumber="1245" 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">
1245
</td>
<td class="diff-line-num new_line old" data-linenumber="1430" 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="LC1245" 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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<td class="diff-line-num old old_line" data-linenumber="1246" 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">
1246
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<td class="diff-line-num new_line old" data-linenumber="1430" 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="LC1246" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">firstGSeqHeader</span><span class="p">)</span> <span class="p">{</span> <span class="n" style="color: #333;">printGSeqHeader</span><span class="p">(</span><span class="n" style="color: #333;">f_out</span><span class="p">,</span> <span class="n" style="color: #333;">gdata</span><span class="p">);</span> <span class="n" style="color: #333;">firstGSeqHeader</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">false</span><span class="p">;</span> <span class="p">}</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1247" 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">
1247
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<td class="diff-line-num new_line old" data-linenumber="1430" 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="LC1247" class="line" lang="cpp"> <span class="n" style="color: #333;">gfst</span><span class="p">.</span><span class="n" style="color: #333;">printGxf</span><span class="p">(</span><span class="n" style="color: #333;">f_out</span><span class="p">,</span> <span class="n" style="color: #333;">exonPrinting</span><span class="p">,</span> <span class="n" style="color: #333;">tracklabel</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="n" style="color: #333;">decodeChars</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1248" 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">
1248
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<pre style="margin: 0;">-<span id="LC1248" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1430" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1430
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<pre style="margin: 0;">+<span id="LC1430" 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 new old_line" data-linenumber="1249" style="width: 35px; color: rgba(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="1431" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1431
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<pre style="margin: 0;">+<span id="LC1431" 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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<td class="diff-line-num new new_line" data-linenumber="1432" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1432
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<pre style="margin: 0;">+<span id="LC1432" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">firstGSeqHeader</span><span class="p">)</span> <span class="p">{</span> <span class="n" style="color: #333;">printGSeqHeader</span><span class="p">(</span><span class="n" style="color: #333;">f_out</span><span class="p">,</span> <span class="n" style="color: #333;">gdata</span><span class="p">);</span> <span class="n" style="color: #333;">firstGSeqHeader</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">false</span><span class="p">;</span> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1433" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1433
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<pre style="margin: 0;">+<span id="LC1433" class="line" lang="cpp"> <span class="n" style="color: #333;">gfst</span><span class="p">.</span><span class="n" style="color: #333;">printGxf</span><span class="p">(</span><span class="n" style="color: #333;">f_out</span><span class="p">,</span> <span class="n" style="color: #333;">exonPrinting</span><span class="p">,</span> <span class="n" style="color: #333;">tracklabel</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="n" style="color: #333;">decodeChars</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1434" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1434
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<pre style="margin: 0;">+<span id="LC1434" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1435" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1435
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<pre style="margin: 0;">+<span id="LC1435" class="line" lang="cpp"> <span class="n" style="color: #333;">printGxfTab</span><span class="p">(</span><span class="n" style="color: #333;">f_out</span><span class="p">,</span> <span class="n" style="color: #333;">gfst</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1436" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1436
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<pre style="margin: 0;">+<span id="LC1436" class="line" lang="cpp"> <span class="p">}</span></span>
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1249
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1437
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<pre style="margin: 0;"> <span id="LC1437" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">gfs_i</span><span class="p">;</span></span>
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1250
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1438
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<pre style="margin: 0;"> <span id="LC1438" class="line" lang="cpp"> <span class="p">}</span></span>
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1251
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1439
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<pre style="margin: 0;"> <span id="LC1439" class="line" lang="cpp"> <span class="p">}</span></span>
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