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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/gffread">Debian Med / gffread</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/gffread/-/commit/5a4e42324053e43df4ec1dbaddb1451367ba0f60">5a4e4232</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2021-10-13T15:53:48+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix watchfile to detect new versions on github
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/gffread/-/commit/a9c3e4d652359021afb42c324503e3dc2e3b438f">a9c3e4d6</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2021-10-13T15:53:51+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: New upstream version
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/gffread/-/commit/3f7ba6a22a42846c56f89697438f164f37ae33d9">3f7ba6a2</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2021-10-13T15:53:52+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 0.12.7</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/gffread/-/commit/b86854ccd280b30d31752bc61105c967deb9427e">b86854cc</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2021-10-13T15:53:54+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/0.12.7'
Update to upstream version '0.12.7'
with Debian dir 525098e5391d2a81a7c52c94cdc88ec640a6d7ff</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/gffread/-/commit/8f12a25e53cdf38e37b213019bda2257d398442e">8f12a25e</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2021-10-13T15:53:54+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Standards-Version: 4.6.0
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/gffread/-/commit/eec571892fac5260ab1590cdd3c9c19dd302dc9c">eec57189</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2021-10-13T16:48:32+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Refresh patches and cleanup changelog
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/gffread/-/commit/8ac3fe2bb5cf710ae7f4f58dd115b827422c973a">8ac3fe2b</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2021-10-13T17:11:22+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Restrictions: allow-stderr
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/gffread/-/commit/852c8655e87bcaf4d8a1f48edb5d2f9ee6c682fb">852c8655</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2021-10-13T17:14:09+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to unstable
</pre>
</li>
</ul>
<h4>11 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#836efb6e25a091dcb4ff8e1dbb2f0be6a5cbf14c">
Makefile
</a>
</li>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
</a>
</li>
<li class="file-stats">
<a href="#3631b3210de1caa2caafc8366d6efc6d87696ea3">
debian/patches/gclib.patch
</a>
</li>
<li class="file-stats">
<a href="#d6c09299b1f914372840e8fd6fcc850f8a11b236">
debian/patches/hardening
</a>
</li>
<li class="file-stats">
<a href="#83223a554d33ba7e1888274ff8ac43adb8147ba0">
debian/tests/control
</a>
</li>
<li class="file-stats">
<a href="#68ef9f98c01c7eecd4c605cc26048a06f3304b79">
debian/watch
</a>
</li>
<li class="file-stats">
<a href="#2e62d67be9b972fb94be4079924f65c3df9a24ac">
gff_utils.cpp
</a>
</li>
<li class="file-stats">
<a href="#70793cbfea41a48621c826d9f427c35d8ef91e5f">
gff_utils.h
</a>
</li>
<li class="file-stats">
<a href="#037bd3173d312d85c9ae5e3fa8f48a79706aa6fb">
gffread.cpp
</a>
</li>
<li class="file-stats">
<a href="#ad76bfab75291d38945f9d9d0587235d3770a87c">
prep_source.sh
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="836efb6e25a091dcb4ff8e1dbb2f0be6a5cbf14c">
<a href="https://salsa.debian.org/med-team/gffread/-/compare/b60b67e61264f6b52333bdea38f528e59e0e08ce...852c8655e87bcaf4d8a1f48edb5d2f9ee6c682fb#836efb6e25a091dcb4ff8e1dbb2f0be6a5cbf14c"><strong>Makefile</strong></a>
<hr>
<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -9,9 +9,9 @@ LINKER := $(if $(LINKER),$(LINKER),g++)</td>
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<td class="old_line diff-line-num" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
9
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<td class="new_line diff-line-num" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC9" class="line" lang="make"></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10
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<td class="new_line diff-line-num" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<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="nf" style="color: #900; font-weight: 600;">$(</span><span class="nb" style="color: #0086b3;">if</span> <span class="nv" style="color: #008080;">$(LDFLAGS)</span>,<span class="nv" style="color: #008080;">$(LDFLAGS)</span>,-g<span class="nf" style="color: #900; font-weight: 600;">)</span></span>
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<td class="old_line diff-line-num" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
11
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<td class="new_line diff-line-num" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="make"></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="new_line diff-line-num old" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="make"><span class="nv" style="color: #008080;">BASEFLAGS</span> <span class="o" style="font-weight: 600;">:=</span> <span class="nt" style="color: #000080;">-Wall</span> <span class="nt" style="color: #000080;">-Wextra</span> <span class="nv" style="color: #008080;">${SEARCHDIRS}</span> <span class="nt" style="color: #000080;">-D_FILE_OFFSET_BITS</span><span class="o" style="font-weight: 600;">=</span>64 <span class="se" style="color: #d14;">\</span></span>
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<td class="old_line diff-line-num 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">
13
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<td class="new_line diff-line-num old" data-linenumber="12" 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="se" style="color: #d14;">\</span></span>
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<td class="old_line diff-line-num old" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
14
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="make"><span class="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++11</span> <span class="nt" style="color: #000080;">-fno-exceptions</span> <span class="nt" style="color: #000080;">-fno-rtti</span></span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="12" style="width: 35px; color: rgba(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="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="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++11 </span><span class="nv" style="color: #008080;">${SEARCHDIRS}</span> <span class="nt" style="color: #000080;">-D_FILE_OFFSET_BITS</span><span class="o" style="font-weight: 600;">=</span>64 <span class="se" style="color: #d14;">\</span></span>
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<td class="old_line diff-line-num new" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="make"><span class="idiff left right"> </span><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="new_line diff-line-num new" 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;">-fno-exceptions</span> <span class="nt" style="color: #000080;">-fno-rtti</span></span>
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15
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<td class="new_line diff-line-num" 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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<td class="old_line diff-line-num" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="new_line diff-line-num" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="make"><span class="nv" style="color: #008080;">GCCV8</span> <span class="o" style="font-weight: 600;">:=</span> <span class="nf" style="color: #900; font-weight: 600;">$(</span><span class="nb" style="color: #0086b3;">shell</span> <span class="nb" style="color: #0086b3;">expr</span> <span class="sb" style="color: #d14;">`</span><span class="nv" style="color: #008080;">${CXX}</span> <span class="nt" style="color: #000080;">-dumpversion</span> | <span class="nb" style="color: #0086b3;">cut</span> <span class="nt" style="color: #000080;">-f1</span> <span class="nt" style="color: #000080;">-d</span>.<span class="sb" style="color: #d14;">`</span> <span class="se" style="color: #d14;">\></span><span class="o" style="font-weight: 600;">=</span> 8<span class="nf" style="color: #900; font-weight: 600;">)</span></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="make"><span class="k" style="font-weight: 600;">ifeq</span> <span class="nv" style="color: #008080;">"$(GCCV8)" "1"</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -22,8 +22,12 @@ CXXFLAGS := $(if $(CXXFLAGS),$(BASEFLAGS) $(CXXFLAGS),$(BASEFLAGS))</td>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="make"></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="make"><span class="k" style="font-weight: 600;">ifneq</span> <span class="nv" style="color: #008080;">(,$(filter %release %static, $(MAKECMDGOALS)))</span></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="make"> <span class="c" style="color: #998; font-style: italic;"># -- release build</span></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="make"> <span class="nv" style="color: #008080;">CXXFLAGS</span> <span class="o" style="font-weight: 600;">:=</span> <span class="nt" style="color: #000080;">-g</span> <span class="nt" style="color: #000080;">-O3</span> <span class="nt" style="color: #000080;">-DNDEBUG</span> <span class="nv" style="color: #008080;">$(CXXFLAGS)</span></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="make"><span class="k" style="font-weight: 600;">else</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="make"> <span class="nv" style="color: #008080;">LIBS</span> <span class="o" style="font-weight: 600;">:=</span> </span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="make"> <span class="k" style="font-weight: 600;">ifneq</span> <span class="nv" style="color: #008080;">(,$(findstring static,$(MAKECMDGOALS)))</span></span>
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<pre style="margin: 0;">+<span id="LC27" 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;">-static-libstdc</span>++ <span class="nt" style="color: #000080;">-static-libgcc</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="make"> <span class="k" style="font-weight: 600;">endif</span></span>
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<pre style="margin: 0;">+<span id="LC29" 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;">-O3</span> <span class="nt" style="color: #000080;">-DNDEBUG</span> <span class="nv" style="color: #008080;">$(CXXFLAGS)</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="make"><span class="k" style="font-weight: 600;">else </span><span class="c" style="color: #998; font-style: italic;">#debug builds</span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="make"> <span class="k" style="font-weight: 600;">ifneq</span> <span class="nv" style="color: #008080;">(,$(filter %profile %gprof %prof, $(MAKECMDGOALS)))</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;">-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="LC33" 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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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -75,7 +79,7 @@ OBJS := ${GCLDIR}/GBase.o ${GCLDIR}/GArgs.o ${GCLDIR}/GFaSeqGet.o \</td>
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="make"> </span>
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="make"><span class="nl">.PHONY </span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">all</span></span>
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="make"></span>
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<pre style="margin: 0;">-<span id="LC78" class="line" lang="make"><span class="nl">all release debug memcheck memdebug profile gprof prof</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">../gclib gffread</span></span>
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="make"><span class="nl">all <span class="idiff left right">static </span>release debug memcheck memdebug profile gprof prof</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">../gclib gffread</span></span>
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="make"></span>
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="make"><span class="nl">../gclib</span><span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="make"> git clone https://github.com/gpertea/gclib.git ../gclib</span>
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<a href="https://salsa.debian.org/med-team/gffread/-/compare/b60b67e61264f6b52333bdea38f528e59e0e08ce...852c8655e87bcaf4d8a1f48edb5d2f9ee6c682fb#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">gffread (0.12.<span class="idiff left">4</span>-1) <span class="idiff right">UNRELEASED</span>; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">gffread (0.12.<span class="idiff left">7</span>-1) <span class="idiff right">unstable</span>; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext"> [ Andreas Tille ]</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"> * New upstream version</span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext"> Seems to require a new version of gclib which would mean a transition</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext"> which is to late now</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> * Fix watchfile to detect new versions on github</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> * New upstream version</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> * Standards-Version: 4.6.0 (routine-update)</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> * Autopkgtest: Restrictions: allow-stderr</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> [ Michael R. Crusoe ]</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> * debian/watch: rename downloaded file into something sensible</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> <span class="idiff left">Sun, 17 Jan 2021 18:02:17</span> +0<span class="idiff right">1</span>00</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> <span class="idiff left">Wed, 13 Oct 2021 17:11:28</span> +0<span class="idiff right">2</span>00</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">gffread (0.12.1-4) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"></span>
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<a href="https://salsa.debian.org/med-team/gffread/-/compare/b60b67e61264f6b52333bdea38f528e59e0e08ce...852c8655e87bcaf4d8a1f48edb5d2f9ee6c682fb#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -7,7 +7,7 @@ Section: science</td>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">Priority: optional</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">Build-Depends: debhelper-compat (= 13),</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> libgclib-dev</span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">5.1</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">6.0</span></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/gffread</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/gffread.git</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">Homepage: https://ccb.jhu.edu/software/stringtie/gff.shtml</span>
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<li id="3631b3210de1caa2caafc8366d6efc6d87696ea3">
<a href="https://salsa.debian.org/med-team/gffread/-/compare/b60b67e61264f6b52333bdea38f528e59e0e08ce...852c8655e87bcaf4d8a1f48edb5d2f9ee6c682fb#3631b3210de1caa2caafc8366d6efc6d87696ea3"><strong>debian/patches/gclib.patch</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -4,16 +4,16 @@ Description: Fix build against libgclib</td>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="diff"></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="diff">--- a/Makefile</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/Makefile</span></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff"><span class="p">@@ -7<span class="idiff left">5</span>,7 +7<span class="idiff right">5</span>,7 @@</span> OBJS := ${GCLDIR}/GBase.o ${GCLDIR}/GArg</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="p">@@ -7<span class="idiff left">9</span>,7 +7<span class="idiff right">9</span>,7 @@</span> OBJS := ${GCLDIR}/GBase.o ${GCLDIR}/GArg</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="diff"> .PHONY : all</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-all release debug memcheck memdebug profile gprof prof: ../gclib gffread</span></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+all release debug memcheck memdebug profile gprof prof: gffread</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-all <span class="idiff left right">static </span>release debug memcheck memdebug profile gprof prof: ../gclib gffread</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+all <span class="idiff left right">static </span>release debug memcheck memdebug profile gprof prof: gffread</span></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="diff"> ../gclib:</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="diff"> git clone https://github.com/gpertea/gclib.git ../gclib</span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="diff"><span class="p">@@ -8<span class="idiff left">5</span>,8 +8<span class="idiff right">5</span>,8 @@</span> gffread.o : gff_utils.h $(GCLDIR)/GBase.</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="p">@@ -8<span class="idiff left">9</span>,8 +8<span class="idiff right">9</span>,8 @@</span> gffread.o : gff_utils.h $(GCLDIR)/GBase.</span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="diff"> gff_utils.o : gff_utils.h $(GCLDIR)/gff.h</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="diff"> ${GCLDIR}/gff.o : ${GCLDIR}/gff.h ${GCLDIR}/GFaSeqGet.h ${GCLDIR}/GList.hh</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="diff"> ${GCLDIR}/GFaSeqGet.o : ${GCLDIR}/GFaSeqGet.h</span>
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<a href="https://salsa.debian.org/med-team/gffread/-/compare/b60b67e61264f6b52333bdea38f528e59e0e08ce...852c8655e87bcaf4d8a1f48edb5d2f9ee6c682fb#d6c09299b1f914372840e8fd6fcc850f8a11b236"><strong>debian/patches/hardening</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -4,7 +4,7 @@ Subject: Use CPPFLAGS</td>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="diff">Allows Debian to harden the binary with CPPFLAGS=-Wdate-time -D_FORTIFY_SOURCE=2</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/Makefile</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/Makefile</span></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff"><span class="p">@@ -6<span class="idiff left">5</span>,7 +6<span class="idiff right">5</span>,7 @@</span> endif</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="p">@@ -6<span class="idiff left">9</span>,7 +6<span class="idiff right">9</span>,7 @@</span> endif</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="diff"> #endif</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="diff"> %.o : %.cpp</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -13,7 +13,7 @@ Allows Debian to harden the binary with CPPFLAGS=-Wdate-time -D_FORTIFY_SOURCE=2</td>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="diff"> # C/C++ linker</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="diff"><span class="p">@@ -<span class="idiff left">86</span>,7 +<span class="idiff right">86</span>,7 @@</span> gff_utils.o : gff_utils.h $(GCLDIR)/gff.</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="p">@@ -<span class="idiff left">90</span>,7 +<span class="idiff right">90</span>,7 @@</span> gff_utils.o : gff_utils.h $(GCLDIR)/gff.</span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="diff"> ${GCLDIR}/gff.o : ${GCLDIR}/gff.h ${GCLDIR}/GFaSeqGet.h ${GCLDIR}/GList.hh</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="diff"> ${GCLDIR}/GFaSeqGet.o : ${GCLDIR}/GFaSeqGet.h</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="diff"> gffread: gffread.o gff_utils.o</span>
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<a href="https://salsa.debian.org/med-team/gffread/-/compare/b60b67e61264f6b52333bdea38f528e59e0e08ce...852c8655e87bcaf4d8a1f48edb5d2f9ee6c682fb#83223a554d33ba7e1888274ff8ac43adb8147ba0"><strong>debian/tests/control</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">Tests: run-tests</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">Depends: gffread, bash, augustus-doc, bedtools-test, cnvkit [amd64 arm64 ppc64el], emboss-data, emboss-test, gbrowse, genometools-common, gff2aplot, gff2ps, htslib-test, libbio-graphics-perl, optimir [amd64 arm64 ppc64el], proteinortho [amd64 arm64 ppc64el s390x], python3-gffutils, python3-pybedtools [amd64 arm64 ppc64el], r-bioc-genomicfeatures, r-bioc-gviz, r-bioc-rhtslib, r-bioc-rtracklayer, seqan-apps, spades [amd64], trinityrnaseq-examples, dpkg-dev</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">Restrictions: allow-stderr</span></pre>
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<a href="https://salsa.debian.org/med-team/gffread/-/compare/b60b67e61264f6b52333bdea38f528e59e0e08ce...852c8655e87bcaf4d8a1f48edb5d2f9ee6c682fb#68ef9f98c01c7eecd4c605cc26048a06f3304b79"><strong>debian/watch</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">version=4</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">opts="filenamemangle=s%(?:.*?)?v?(\d[\d.]*)\.tar\.gz%@PACKAGE@-$1.tar.gz%" \</span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext">https://github.com/gpertea/gffread/releases .*/<span class="idiff left right">archive/</span>v?@ANY_VERSION@@ARCHIVE_EXT@</span></pre>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">https://github.com/gpertea/gffread/releases .*/v?@ANY_VERSION@@ARCHIVE_EXT@</span></pre>
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<a href="https://salsa.debian.org/med-team/gffread/-/compare/b60b67e61264f6b52333bdea38f528e59e0e08ce...852c8655e87bcaf4d8a1f48edb5d2f9ee6c682fb#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">@@ -42,10 +42,15 @@ bool fullCDSonly=false; // starts with START, ends with STOP codon</td>
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<pre style="margin: 0;"> <span id="LC42" 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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<pre style="margin: 0;"> <span id="LC43" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">writeExonSegs</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="LC44" 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;">tracklabel</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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<pre style="margin: 0;">+<span id="LC45" 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="LC46" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">char* rfltGSeq=NULL;</span></span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">char rfltStrand=0;</span></span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">uint rfltStart=0;</span></span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="cpp"><span class="n" style="color: #333;">uint</span> <span class="n" style="color: #333;">rfltEnd</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">MAX_UINT</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">uint rfltEnd=MAX_UINT;*/</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="cpp"><span class="n" style="color: #333;">GRangeParser</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">fltRange</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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<pre style="margin: 0;">+<span id="LC51" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="cpp"><span class="n" style="color: #333;">GRangeParser</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">fltJunction</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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<pre style="margin: 0;">+<span id="LC53" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">rfltWithin</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">false</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">//check for full containment within given range</span></span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">addDescr</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="cpp"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -166,7 +171,6 @@ int cmpRedundant(GffObj& a, GffObj& b) {</td>
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<pre style="margin: 0;"> <span id="LC171" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">return</span> <span class="p">(</span><span class="n" style="color: #333;">a</span><span class="p">.</span><span class="n" style="color: #333;">exons</span><span class="p">.</span><span class="n" style="color: #333;">Count</span><span class="p">()</span><span class="o" style="font-weight: 600;">></span><span class="n" style="color: #333;">b</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;">1</span><span class="o" style="font-weight: 600;">:</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC172" class="line" lang="cpp"><span class="p">}</span></span>
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173
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<pre style="margin: 0;"> <span id="LC173" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC169" class="line" lang="cpp"></span>
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174
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<pre style="margin: 0;"> <span id="LC174" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="nf" style="color: #900; font-weight: 600;">tMatch</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;">a</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;">b</span><span class="p">)</span> <span class="p">{</span></span>
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175
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<pre style="margin: 0;"> <span id="LC175" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//strict intron chain match, or single-exon perfect match</span></span>
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172
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176
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<pre style="margin: 0;"> <span id="LC176" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">imax</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">a</span><span class="p">.</span><span class="n" style="color: #333;">exons</span><span class="p">.</span><span class="n" style="color: #333;">Count</span><span class="p">()</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="282" style="width: 35px; color: rgba(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="286" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -282,6 +286,8 @@ int adjust_stopcodon(GffObj& gffrec, int adj, GList<GSeg>* seglst) {</td>
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282
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286
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<pre style="margin: 0;"> <span id="LC286" class="line" lang="cpp"></span>
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283
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287
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<pre style="margin: 0;"> <span id="LC287" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">printTableData</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">FILE</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">f</span><span class="p">,</span> <span class="n" style="color: #333;">GffObj</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">g</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">inFasta</span><span class="p">)</span> <span class="p">{</span></span>
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284
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288
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<pre style="margin: 0;"> <span id="LC288" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//using attribute list in tableCols</span></span>
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289
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<pre style="margin: 0;">+<span id="LC289" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">DBUF_LEN</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1024</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">//there should not be attribute values larger than 1K!</span></span>
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290
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<pre style="margin: 0;">+<span id="LC290" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">dbuf</span><span class="p">[</span><span class="n" style="color: #333;">DBUF_LEN</span><span class="p">];</span></span>
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285
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291
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<pre style="margin: 0;"> <span id="LC291" 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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286
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292
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<pre style="margin: 0;"> <span id="LC292" 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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287
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293
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<pre style="margin: 0;"> <span id="LC293" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">></span><span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">inFasta</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="291" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="297" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -291,7 +297,12 @@ void printTableData(FILE* f, GffObj& g, bool inFasta) {</td>
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291
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297
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<pre style="margin: 0;"> <span id="LC297" 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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292
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298
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<pre style="margin: 0;"> <span id="LC298" 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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293
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299
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<pre style="margin: 0;"> <span id="LC299" 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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294
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<pre style="margin: 0;">-<span id="LC294" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">,</span><span class="s" style="color: #d14;">"%s"</span><span class="p">,</span><span class="n" style="color: #333;">av</span><span class="o" style="font-weight: 600;">!=</span><span class="nb" style="color: #0086b3;">NULL</span><span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">av</span> <span class="o" style="font-weight: 600;">:</span> <span class="s" style="color: #d14;">"."</span><span class="p">);</span></span>
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300
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<pre style="margin: 0;">+<span id="LC300" 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="p">)</span> <span class="p">{</span></span>
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301
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<pre style="margin: 0;">+<span id="LC301" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">decodeChars</span><span class="p">)</span> <span class="p">{</span></span>
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302
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<pre style="margin: 0;">+<span id="LC302" 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;">decodeHexChars</span><span class="p">(</span><span class="n" style="color: #333;">dbuf</span><span class="p">,</span> <span class="n" style="color: #333;">av</span><span class="p">,</span> <span class="n" style="color: #333;">DBUF_LEN</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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303
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<pre style="margin: 0;">+<span id="LC303" 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;">dbuf</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" 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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<pre style="margin: 0;">+<span id="LC304" 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;">"%s"</span><span class="p">,</span><span class="n" style="color: #333;">av</span><span class="p">);</span></span>
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305
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<pre style="margin: 0;">+<span id="LC305" 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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295
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306
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<pre style="margin: 0;"> <span id="LC306" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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296
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307
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<pre style="margin: 0;"> <span id="LC307" 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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297
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308
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<pre style="margin: 0;"> <span id="LC308" 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 unfold js-unfold old_line" data-linenumber="375" style="width: 35px; color: rgba(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="386" style="width: 35px; color: rgba(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">@@ -375,7 +386,9 @@ bool GffLoader::validateGffRec(GffObj* gffrec) {</td>
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375
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386
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<pre style="margin: 0;"> <span id="LC386" class="line" lang="cpp"> <span class="p">}</span></span>
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376
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387
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<pre style="margin: 0;"> <span id="LC387" class="line" lang="cpp"> <span class="p">}</span></span>
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377
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388
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<pre style="margin: 0;"> <span id="LC388" class="line" lang="cpp"> <span class="p">}</span></span>
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389
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<pre style="margin: 0;">+<span id="LC389" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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378
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390
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<pre style="margin: 0;"> <span id="LC390" class="line" lang="cpp"> <span class="p">}</span></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;">gffrec</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">isGene</span><span class="p">()</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">keepGenes</span><span class="p">)</span> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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379
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392
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<pre style="margin: 0;"> <span id="LC392" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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380
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393
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<pre style="margin: 0;"> <span id="LC393" class="line" lang="cpp"> <span class="p">}</span> <span class="c1" style="color: #998; font-style: italic;">//transcript rejected</span></span>
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381
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394
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<pre style="margin: 0;"> <span id="LC394" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="419" style="width: 35px; color: rgba(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="432" style="width: 35px; color: rgba(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">@@ -419,24 +432,24 @@ bool GffLoader::checkFilters(GffObj* gffrec) {</td>
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419
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432
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<pre style="margin: 0;"> <span id="LC432" class="line" lang="cpp"> <span class="n" style="color: #333;">gffrec</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getID</span><span class="p">(),</span> <span class="n" style="color: #333;">minLen</span><span class="p">);</span></span>
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420
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433
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<pre style="margin: 0;"> <span id="LC433" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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421
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434
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<pre style="margin: 0;"> <span id="LC434" class="line" lang="cpp"> <span class="p">}</span></span>
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422
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<pre style="margin: 0;">-<span id="LC422" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">r</span>flt<span class="idiff right">GSeq</span></span><span class="o" style="font-weight: 600;">!=</span><span class="nb" style="color: #0086b3;">NULL</span><span class="p">)</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">//filter by gseqName</span></span>
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423
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<pre style="margin: 0;">-<span id="LC423" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">strcmp</span><span class="p">(</span><span class="n" style="color: #333;">gffrec</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getGSeqName</span><span class="p">(),</span><span class="n" style="color: #333;"><span class="idiff left">r</span>flt<span class="idiff right">GSeq</span></span><span class="p">)</span><span class="o" style="font-weight: 600;">!=</span><span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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435
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<pre style="margin: 0;">+<span id="LC435" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">flt<span class="idiff left right">Range</span></span><span class="o" style="font-weight: 600;">!=</span><span class="nb" style="color: #0086b3;">NULL</span><span class="p">)</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">//filter by gseqName</span></span>
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436
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<pre style="margin: 0;">+<span id="LC436" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">fltRange</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">refName</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="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff"> </span><span class="n" style="color: #333;">strcmp</span><span class="p">(</span><span class="n" style="color: #333;">gffrec</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getGSeqName</span><span class="p">(),</span><span class="n" style="color: #333;">flt<span class="idiff">Range</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff right">refName</span></span><span class="p">)</span><span class="o" style="font-weight: 600;">!=</span><span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC437" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC438" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC426" class="line" lang="cpp"> <span class="p">}</span></span>
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427
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<pre style="margin: 0;">-<span id="LC427" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">rfltStrand</span><span class="o" style="font-weight: 600;">></span><span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">gffrec</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">strand</span> <span class="o" style="font-weight: 600;">!=</span><span class="n" style="color: #333;">rfltStrand</span><span class="p">)</span> <span class="p">{</span></span>
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428
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<pre style="margin: 0;">-<span id="LC428" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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429
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<pre style="margin: 0;">-<span id="LC429" class="line" lang="cpp"> <span class="p">}</span></span>
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430
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<pre style="margin: 0;">-<span id="LC430" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//check coordinates</span></span>
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431
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<pre style="margin: 0;">-<span id="LC431" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">rfltStart</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;">rfltEnd</span><span class="o" style="font-weight: 600;">!=</span><span class="n" style="color: #333;">MAX_UINT</span><span class="p">)</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;">rfltWithin</span><span class="p">)</span> <span class="p">{</span></span>
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433
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<pre style="margin: 0;">-<span id="LC433" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">gffrec</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">start</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">rfltStart</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">gffrec</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">end</span><span class="o" style="font-weight: 600;">></span><span class="n" style="color: #333;">rfltEnd</span><span class="p">)</span> <span class="p">{</span></span>
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434
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<pre style="margin: 0;">-<span id="LC434" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">//not within query range</span></span>
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<pre style="margin: 0;">-<span id="LC435" class="line" lang="cpp"> <span class="p">}</span></span>
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439
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<pre style="margin: 0;">+<span id="LC439" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">fltRange</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="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">gffrec</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">strand</span><span class="o" style="font-weight: 600;">!=</span><span class="n" style="color: #333;">fltRange</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">strand</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC440" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC441" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC437" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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438
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<pre style="margin: 0;">-<span id="LC438" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">gffrec</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">start</span><span class="o" style="font-weight: 600;">></span><span class="n" style="color: #333;">rfltEnd</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">gffrec</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">end</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">rfltStart</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC439" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC442" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//check coordinates</span></span>
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<pre style="margin: 0;">+<span id="LC443" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">fltRange</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;">fltRange</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;">UINT_MAX</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC444" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">rfltWithin</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC445" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">gffrec</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">start</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">fltRange</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;">gffrec</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;">fltRange</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">end</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC446" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">//not within query range</span></span>
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<pre style="margin: 0;">+<span id="LC447" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC448" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC449" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC450" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">gffrec</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;">fltRange</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;">gffrec</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;">fltRange</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="LC451" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC452" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC453" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC454" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC455" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -444,7 +457,6 @@ bool GffLoader::checkFilters(GffObj* gffrec) {</td>
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<pre style="margin: 0;"> <span id="LC457" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//remove attributes that are not in attrList</span></span>
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<pre style="margin: 0;"> <span id="LC458" class="line" lang="cpp"> <span class="n" style="color: #333;">gffrec</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">removeAttrs</span><span class="p">(</span><span class="n" style="color: #333;">attrList</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC459" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC447" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC460" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">gffrec</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">isTranscript</span><span class="p">())</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">// && TFilters) ?</span></span>
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<pre style="margin: 0;"> <span id="LC461" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//these filters only apply to transcripts</span></span>
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462
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<pre style="margin: 0;"> <span id="LC462" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">multiExon</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">gffrec</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">exons</span><span class="p">.</span><span class="n" style="color: #333;">Count</span><span class="p">()</span><span class="o" style="font-weight: 600;"><=</span><span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -454,12 +466,46 @@ bool GffLoader::checkFilters(GffObj* gffrec) {</td>
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<pre style="margin: 0;"> <span id="LC466" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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467
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<pre style="margin: 0;"> <span id="LC467" class="line" lang="cpp"> <span class="p">}</span></span>
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456
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468
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<pre style="margin: 0;"> <span id="LC468" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">wNConly</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">gffrec</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">hasCDS</span><span class="p">())</span> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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469
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<pre style="margin: 0;">+<span id="LC469" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">fltJunction</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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470
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<pre style="margin: 0;">+<span id="LC470" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">gffrec</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">exons</span><span class="p">.</span><span class="n" style="color: #333;">Count</span><span class="p">()</span><span class="o" style="font-weight: 600;"><=</span><span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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471
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<pre style="margin: 0;">+<span id="LC471" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">fltJunction</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">refName</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;">strcmp</span><span class="p">(</span><span class="n" style="color: #333;">gffrec</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getGSeqName</span><span class="p">(),</span><span class="n" style="color: #333;">fltJunction</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">refName</span><span class="p">)</span><span class="o" style="font-weight: 600;">!=</span><span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC472" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC473" class="line" lang="cpp"> <span class="p">}</span></span>
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474
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<pre style="margin: 0;">+<span id="LC474" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">fltJunction</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;">gffrec</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;">fltJunction</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">strand</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC475" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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476
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<pre style="margin: 0;">+<span id="LC476" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC477" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//check coordinates</span></span>
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478
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<pre style="margin: 0;">+<span id="LC478" class="line" lang="cpp"> <span class="n" style="color: #333;">uint</span> <span class="n" style="color: #333;">jstart</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">fltJunction</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">start</span><span class="p">;</span></span>
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479
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<pre style="margin: 0;">+<span id="LC479" class="line" lang="cpp"> <span class="n" style="color: #333;">uint</span> <span class="n" style="color: #333;">jend</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">fltJunction</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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480
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<pre style="margin: 0;">+<span id="LC480" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">jstart</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;">jstart</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">jend</span><span class="p">;</span></span>
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481
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<pre style="margin: 0;">+<span id="LC481" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">jend</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;">jend</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">jstart</span><span class="p">;</span></span>
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482
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<pre style="margin: 0;">+<span id="LC482" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">gffrec</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">start</span><span class="o" style="font-weight: 600;">>=</span><span class="n" style="color: #333;">jstart</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">gffrec</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">end</span><span class="o" style="font-weight: 600;"><=</span><span class="n" style="color: #333;">jend</span><span class="p">)</span> <span class="p">{</span></span>
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483
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<pre style="margin: 0;">+<span id="LC483" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC484" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC485" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC486" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">noJMatch</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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487
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<pre style="margin: 0;">+<span id="LC487" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">gffrec</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">exons</span><span class="p">.</span><span class="n" style="color: #333;">Count</span><span class="p">()</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span><span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="p">{</span></span>
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488
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<pre style="margin: 0;">+<span id="LC488" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">fltJunction</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;">fltJunction</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">end</span><span class="p">)</span> <span class="p">{</span></span>
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489
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<pre style="margin: 0;">+<span id="LC489" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">gffrec</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">exons</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">end</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">==</span><span class="n" style="color: #333;">fltJunction</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>
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490
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<pre style="margin: 0;">+<span id="LC490" class="line" lang="cpp"> <span class="n" style="color: #333;">gffrec</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">exons</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">start</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">==</span><span class="n" style="color: #333;">fltJunction</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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491
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<pre style="margin: 0;">+<span id="LC491" class="line" lang="cpp"> <span class="p">{</span> <span class="n" style="color: #333;">noJMatch</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">false</span><span class="p">;</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span> <span class="p">}</span></span>
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492
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<pre style="margin: 0;">+<span id="LC492" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">fltJunction</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 class="c1" style="color: #998; font-style: italic;">//end match not required</span></span>
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493
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<pre style="margin: 0;">+<span id="LC493" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">gffrec</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">exons</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">end</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">==</span><span class="n" style="color: #333;">fltJunction</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">start</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC494" class="line" lang="cpp"> <span class="p">{</span> <span class="n" style="color: #333;">noJMatch</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">false</span><span class="p">;</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC495" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">//only end match required:</span></span>
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496
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<pre style="margin: 0;">+<span id="LC496" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">gffrec</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">exons</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">start</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">==</span><span class="n" style="color: #333;">fltJunction</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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<pre style="margin: 0;">+<span id="LC497" class="line" lang="cpp"> <span class="p">{</span> <span class="n" style="color: #333;">noJMatch</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">false</span><span class="p">;</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span> <span class="p">}</span></span>
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498
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<pre style="margin: 0;">+<span id="LC498" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC499" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC500" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">noJMatch</span><span class="p">)</span> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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501
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<pre style="margin: 0;">+<span id="LC501" class="line" lang="cpp"> <span class="p">}</span></span>
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502
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<pre style="margin: 0;">+<span id="LC502" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC503" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">process_transcript</span><span class="p">(</span><span class="n" style="color: #333;">gfasta</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">gffrec</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC504" class="line" lang="cpp"> <span class="p">}</span> <span class="c1" style="color: #998; font-style: italic;">//transcript filters check</span></span>
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<pre style="margin: 0;"> <span id="LC505" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC506" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC507" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC462" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="nf" style="color: #900; font-weight: 600;">process_transcript</span><span class="p">(</span><span class="n" style="color: #333;">GFastaDb</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">gfasta</span><span class="p">,</span> <span class="n" style="color: #333;">GffObj</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">gffrec</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC508" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;"><span class="idiff left">GffLoader</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">::</span></span><span class="n" style="color: #333;">process_transcript</span><span class="p">(</span><span class="n" style="color: #333;">GFastaDb</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">gfasta</span><span class="p">,</span> <span class="n" style="color: #333;">GffObj</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">gffrec</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC509" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">gffrec</span><span class="p">.</span><span class="n" style="color: #333;">isTranscript</span><span class="p">())</span> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">//shouldn't call this function unless it's a transcript</span></span>
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<pre style="margin: 0;"> <span id="LC510" 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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<pre style="margin: 0;"> <span id="LC511" 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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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="726" style="width: 35px; color: rgba(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">@@ -680,40 +726,48 @@ bool process_transcript(GFastaDb& gfasta, GffObj& gffrec) {</td>
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<pre style="margin: 0;"> <span id="LC726" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> if (adjstop!=NULL) delete adjstop;</span></span>
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<pre style="margin: 0;"> <span id="LC727" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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728
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<pre style="margin: 0;"> <span id="LC728" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">cdsnt</span><span class="o" style="font-weight: 600;">!=</span><span class="nb" style="color: #0086b3;">NULL</span><span class="p">)</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">// && !inframeStop) {</span></span>
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729
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<pre style="margin: 0;">+<span id="LC729" class="line" lang="cpp"> <span class="n" style="color: #333;">GStr</span> <span class="n" style="color: #333;">defline</span><span class="p">(</span><span class="n" style="color: #333;">gffrec</span><span class="p">.</span><span class="n" style="color: #333;">getID</span><span class="p">(),</span> <span class="mi" style="color: #099;">94</span><span class="p">);</span></span>
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730
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<pre style="margin: 0;">+<span id="LC730" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">writeExonSegs</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC731" class="line" lang="cpp"> <span class="n" style="color: #333;">defline</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="s" style="color: #d14;">" loc:"</span><span class="p">);</span></span>
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732
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<pre style="margin: 0;">+<span id="LC732" class="line" lang="cpp"> <span class="n" style="color: #333;">defline</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">gffrec</span><span class="p">.</span><span class="n" style="color: #333;">getGSeqName</span><span class="p">());</span></span>
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733
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<pre style="margin: 0;">+<span id="LC733" class="line" lang="cpp"> <span class="n" style="color: #333;">defline</span><span class="p">.</span><span class="n" style="color: #333;">appendfmt</span><span class="p">(</span><span class="s" style="color: #d14;">"(%c)"</span><span class="p">,</span><span class="n" style="color: #333;">gffrec</span><span class="p">.</span><span class="n" style="color: #333;">strand</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC734" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//warning: not CDS coordinates are written here, but the exon ones</span></span>
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735
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<pre style="margin: 0;">+<span id="LC735" class="line" lang="cpp"> <span class="n" style="color: #333;">defline</span><span class="o" style="font-weight: 600;">+=</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)</span><span class="n" style="color: #333;">gffrec</span><span class="p">.</span><span class="n" style="color: #333;">start</span><span class="p">;</span></span>
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736
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<pre style="margin: 0;">+<span id="LC736" class="line" lang="cpp"> <span class="n" style="color: #333;">defline</span><span class="o" style="font-weight: 600;">+=</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="p">)</span><span class="sc" style="color: #d14;">'-'</span><span class="p">;</span></span>
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737
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<pre style="margin: 0;">+<span id="LC737" class="line" lang="cpp"> <span class="n" style="color: #333;">defline</span><span class="o" style="font-weight: 600;">+=</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)</span><span class="n" style="color: #333;">gffrec</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">;</span></span>
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738
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<pre style="margin: 0;">+<span id="LC738" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// -- here these are CDS substring coordinates on the spliced sequence:</span></span>
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739
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<pre style="margin: 0;">+<span id="LC739" class="line" lang="cpp"> <span class="n" style="color: #333;">defline</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="s" style="color: #d14;">" segs:"</span><span class="p">);</span></span>
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740
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<pre style="margin: 0;">+<span id="LC740" class="line" lang="cpp"> <span class="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;">seglst</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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741
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<pre style="margin: 0;">+<span id="LC741" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="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;">defline</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="s" style="color: #d14;">","</span><span class="p">);</span></span>
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742
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<pre style="margin: 0;">+<span id="LC742" class="line" lang="cpp"> <span class="n" style="color: #333;">defline</span><span class="o" style="font-weight: 600;">+=</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)</span><span class="n" style="color: #333;">seglst</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">start</span><span class="p">;</span></span>
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743
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<pre style="margin: 0;">+<span id="LC743" class="line" lang="cpp"> <span class="n" style="color: #333;">defline</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="s" style="color: #d14;">"-"</span><span class="p">);</span></span>
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744
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<pre style="margin: 0;">+<span id="LC744" class="line" lang="cpp"> <span class="n" style="color: #333;">defline</span><span class="o" style="font-weight: 600;">+=</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)</span><span class="n" style="color: #333;">seglst</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">end</span><span class="p">;</span></span>
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745
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<pre style="margin: 0;">+<span id="LC745" class="line" lang="cpp"> <span class="p">}</span></span>
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746
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<pre style="margin: 0;">+<span id="LC746" class="line" lang="cpp"> <span class="p">}</span></span>
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683
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747
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<pre style="margin: 0;"> <span id="LC747" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">f_y</span><span class="o" style="font-weight: 600;">!=</span><span class="nb" style="color: #0086b3;">NULL</span><span class="p">)</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">//CDS translation fasta output requested</span></span>
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684
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748
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<pre style="margin: 0;"> <span id="LC748" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">cdsaa</span><span class="o" style="font-weight: 600;">==</span><span class="nb" style="color: #0086b3;">NULL</span><span class="p">)</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">//translate now if not done before</span></span>
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685
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749
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<pre style="margin: 0;"> <span id="LC749" class="line" lang="cpp"> <span class="n" style="color: #333;">cdsaa</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">translateDNA</span><span class="p">(</span><span class="n" style="color: #333;">cdsnt</span><span class="p">,</span> <span class="n" style="color: #333;">aalen</span><span class="p">,</span> <span class="n" style="color: #333;">seqlen</span><span class="p">);</span></span>
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686
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750
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<pre style="margin: 0;"> <span id="LC750" class="line" lang="cpp"> <span class="p">}</span></span>
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687
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751
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<pre style="margin: 0;"> <span id="LC751" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">aalen</span><span class="o" style="font-weight: 600;">></span><span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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688
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752
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<pre style="margin: 0;"> <span id="LC752" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">cdsaa</span><span class="p">[</span><span class="n" style="color: #333;">aalen</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">==</span><span class="sc" style="color: #d14;">'.'</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">cdsaa</span><span class="p">[</span><span class="n" style="color: #333;">aalen</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">==</span><span class="sc" style="color: #d14;">'\0'</span><span class="p">)</span> <span class="o" style="font-weight: 600;">--</span><span class="n" style="color: #333;">aalen</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">//avoid printing the stop codon</span></span>
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689
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<pre style="margin: 0;">-<span id="LC689" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">f_y</span><span class="p">,</span> <span class="s" style="color: #d14;">">%s"</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">gffrec</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">getID</span></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="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">f_y</span><span class="p">,</span> <span class="s" style="color: #d14;">">%s"</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">defline</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">chars</span></span><span class="p">());</span></span>
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690
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754
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<pre style="margin: 0;"> <span id="LC754" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">fmtTable</span><span class="p">)</span> <span class="n" style="color: #333;">printTableData</span><span class="p">(</span><span class="n" style="color: #333;">f_y</span><span class="p">,</span> <span class="n" style="color: #333;">gffrec</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">);</span></span>
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691
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<pre style="margin: 0;">-<span id="LC691" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">f_y</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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755
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<pre style="margin: 0;">+<span id="LC755" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</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="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">gffrec</span><span class="p">.</span><span class="n" style="color: #333;">attrs</span><span class="o" style="font-weight: 600;">!=</span><span class="nb" style="color: #0086b3;">NULL</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">gffrec</span><span class="p">.</span><span class="n" style="color: #333;">attrs</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Count</span><span class="p">()</span><span class="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_y</span><span class="p">,</span><span class="s" style="color: #d14;">" "</span><span class="p">);</span></span>
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757
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<pre style="margin: 0;">+<span id="LC757" class="line" lang="cpp"> <span class="n" style="color: #333;">gffrec</span><span class="p">.</span><span class="n" style="color: #333;">printAttrs</span><span class="p">(</span><span class="n" style="color: #333;">f_y</span><span class="p">,</span> <span class="s" style="color: #d14;">";"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">,</span> <span class="n" style="color: #333;">decodeChars</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">);</span></span>
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758
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<pre style="margin: 0;">+<span id="LC758" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">f_y</span><span class="p">,</span> <span class="s" style="color: #d14;">"</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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759
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<pre style="margin: 0;">+<span id="LC759" class="line" lang="cpp"> <span class="p">}</span></span>
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692
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760
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<pre style="margin: 0;"> <span id="LC760" class="line" lang="cpp"> <span class="n" style="color: #333;">printFasta</span><span class="p">(</span><span class="n" style="color: #333;">f_y</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="n" style="color: #333;">cdsaa</span><span class="p">,</span> <span class="n" style="color: #333;">aalen</span><span class="p">,</span> <span class="n" style="color: #333;">StarStop</span><span class="p">);</span></span>
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693
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761
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<pre style="margin: 0;"> <span id="LC761" class="line" lang="cpp"> <span class="p">}</span></span>
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694
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762
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<pre style="margin: 0;"> <span id="LC762" class="line" lang="cpp"> <span class="p">}</span></span>
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695
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763
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<pre style="margin: 0;"> <span id="LC763" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">f_x</span><span class="o" style="font-weight: 600;">!=</span><span class="nb" style="color: #0086b3;">NULL</span><span class="p">)</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">//CDS only</span></span>
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696
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<pre style="margin: 0;">-<span id="LC696" class="line" lang="cpp"> <span class="n" style="color: #333;">GStr</span> <span class="n" style="color: #333;">defline</span><span class="p">(</span><span class="n" style="color: #333;">gffrec</span><span class="p">.</span><span class="n" style="color: #333;">getID</span><span class="p">(),</span> <span class="mi" style="color: #099;">94</span><span class="p">);</span></span>
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697
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<pre style="margin: 0;">-<span id="LC697" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">writeExonSegs</span><span class="p">)</span> <span class="p">{</span></span>
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698
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<pre style="margin: 0;">-<span id="LC698" class="line" lang="cpp"> <span class="n" style="color: #333;">defline</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="s" style="color: #d14;">" loc:"</span><span class="p">);</span></span>
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699
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<pre style="margin: 0;">-<span id="LC699" class="line" lang="cpp"> <span class="n" style="color: #333;">defline</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">gffrec</span><span class="p">.</span><span class="n" style="color: #333;">getGSeqName</span><span class="p">());</span></span>
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700
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<pre style="margin: 0;">-<span id="LC700" class="line" lang="cpp"> <span class="n" style="color: #333;">defline</span><span class="p">.</span><span class="n" style="color: #333;">appendfmt</span><span class="p">(</span><span class="s" style="color: #d14;">"(%c)"</span><span class="p">,</span><span class="n" style="color: #333;">gffrec</span><span class="p">.</span><span class="n" style="color: #333;">strand</span><span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="701" 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">
701
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<pre style="margin: 0;">-<span id="LC701" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//warning: not CDS coordinates are written here, but the exon ones</span></span>
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702
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<pre style="margin: 0;">-<span id="LC702" class="line" lang="cpp"> <span class="n" style="color: #333;">defline</span><span class="o" style="font-weight: 600;">+=</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)</span><span class="n" style="color: #333;">gffrec</span><span class="p">.</span><span class="n" style="color: #333;">start</span><span class="p">;</span></span>
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703
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<pre style="margin: 0;">-<span id="LC703" class="line" lang="cpp"> <span class="n" style="color: #333;">defline</span><span class="o" style="font-weight: 600;">+=</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="p">)</span><span class="sc" style="color: #d14;">'-'</span><span class="p">;</span></span>
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704
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<pre style="margin: 0;">-<span id="LC704" class="line" lang="cpp"> <span class="n" style="color: #333;">defline</span><span class="o" style="font-weight: 600;">+=</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)</span><span class="n" style="color: #333;">gffrec</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC705" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// -- here these are CDS substring coordinates on the spliced sequence:</span></span>
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<pre style="margin: 0;">-<span id="LC706" class="line" lang="cpp"> <span class="n" style="color: #333;">defline</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="s" style="color: #d14;">" segs:"</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC707" 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;">seglst</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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<pre style="margin: 0;">-<span id="LC708" 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;">defline</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="s" style="color: #d14;">","</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC709" class="line" lang="cpp"> <span class="n" style="color: #333;">defline</span><span class="o" style="font-weight: 600;">+=</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)</span><span class="n" style="color: #333;">seglst</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">start</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC710" class="line" lang="cpp"> <span class="n" style="color: #333;">defline</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="s" style="color: #d14;">"-"</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC711" class="line" lang="cpp"> <span class="n" style="color: #333;">defline</span><span class="o" style="font-weight: 600;">+=</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)</span><span class="n" style="color: #333;">seglst</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">end</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC712" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC713" class="line" lang="cpp"> <span class="p">}</span></span>
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764
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<pre style="margin: 0;"> <span id="LC764" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">f_x</span><span class="p">,</span> <span class="s" style="color: #d14;">">%s"</span><span class="p">,</span> <span class="n" style="color: #333;">defline</span><span class="p">.</span><span class="n" style="color: #333;">chars</span><span class="p">());</span></span>
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765
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<pre style="margin: 0;"> <span id="LC765" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">fmtTable</span><span class="p">)</span> <span class="n" style="color: #333;">printTableData</span><span class="p">(</span><span class="n" style="color: #333;">f_x</span><span class="p">,</span> <span class="n" style="color: #333;">gffrec</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">);</span></span>
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716
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<pre style="margin: 0;">-<span id="LC716" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">f_x</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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766
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<pre style="margin: 0;">+<span id="LC766" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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767
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<pre style="margin: 0;">+<span id="LC767" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">gffrec</span><span class="p">.</span><span class="n" style="color: #333;">attrs</span><span class="o" style="font-weight: 600;">!=</span><span class="nb" style="color: #0086b3;">NULL</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">gffrec</span><span class="p">.</span><span class="n" style="color: #333;">attrs</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Count</span><span class="p">()</span><span class="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_x</span><span class="p">,</span><span class="s" style="color: #d14;">" "</span><span class="p">);</span></span>
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768
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<pre style="margin: 0;">+<span id="LC768" class="line" lang="cpp"> <span class="n" style="color: #333;">gffrec</span><span class="p">.</span><span class="n" style="color: #333;">printAttrs</span><span class="p">(</span><span class="n" style="color: #333;">f_x</span><span class="p">,</span> <span class="s" style="color: #d14;">";"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">,</span> <span class="n" style="color: #333;">decodeChars</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">);</span></span>
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769
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<pre style="margin: 0;">+<span id="LC769" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">f_x</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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770
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<pre style="margin: 0;">+<span id="LC770" class="line" lang="cpp"> <span class="p">}</span></span>
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717
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771
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<pre style="margin: 0;"> <span id="LC771" class="line" lang="cpp"> <span class="n" style="color: #333;">printFasta</span><span class="p">(</span><span class="n" style="color: #333;">f_x</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="n" style="color: #333;">cdsnt</span><span class="p">,</span> <span class="n" style="color: #333;">seqlen</span><span class="p">);</span></span>
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718
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772
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<pre style="margin: 0;"> <span id="LC772" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC773" class="line" lang="cpp"> <span class="n" style="color: #333;">GFREE</span><span class="p">(</span><span class="n" style="color: #333;">cdsnt</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="829" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -775,7 +829,11 @@ bool process_transcript(GFastaDb& gfasta, GffObj& gffrec) {</td>
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775
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829
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<pre style="margin: 0;"> <span id="LC829" class="line" lang="cpp"></span>
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830
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<pre style="margin: 0;"> <span id="LC830" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">f_w</span><span class="p">,</span> <span class="s" style="color: #d14;">">%s"</span><span class="p">,</span> <span class="n" style="color: #333;">defline</span><span class="p">.</span><span class="n" style="color: #333;">chars</span><span class="p">());</span></span>
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777
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831
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<pre style="margin: 0;"> <span id="LC831" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">fmtTable</span><span class="p">)</span> <span class="n" style="color: #333;">printTableData</span><span class="p">(</span><span class="n" style="color: #333;">f_w</span><span class="p">,</span> <span class="n" style="color: #333;">gffrec</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">);</span></span>
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778
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<pre style="margin: 0;">-<span id="LC778" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">f_w</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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832
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<pre style="margin: 0;">+<span id="LC832" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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833
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<pre style="margin: 0;">+<span id="LC833" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">gffrec</span><span class="p">.</span><span class="n" style="color: #333;">attrs</span><span class="o" style="font-weight: 600;">!=</span><span class="nb" style="color: #0086b3;">NULL</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">gffrec</span><span class="p">.</span><span class="n" style="color: #333;">attrs</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Count</span><span class="p">()</span><span class="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_w</span><span class="p">,</span><span class="s" style="color: #d14;">" "</span><span class="p">);</span></span>
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834
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<pre style="margin: 0;">+<span id="LC834" class="line" lang="cpp"> <span class="n" style="color: #333;">gffrec</span><span class="p">.</span><span class="n" style="color: #333;">printAttrs</span><span class="p">(</span><span class="n" style="color: #333;">f_w</span><span class="p">,</span> <span class="s" style="color: #d14;">";"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">,</span> <span class="n" style="color: #333;">decodeChars</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">);</span></span>
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835
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<pre style="margin: 0;">+<span id="LC835" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">f_w</span><span class="p">,</span> <span class="s" style="color: #d14;">"</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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836
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<pre style="margin: 0;">+<span id="LC836" class="line" lang="cpp"> <span class="p">}</span></span>
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837
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<pre style="margin: 0;"> <span id="LC837" class="line" lang="cpp"> <span class="n" style="color: #333;">printFasta</span><span class="p">(</span><span class="n" style="color: #333;">f_w</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="n" style="color: #333;">exont</span><span class="p">,</span> <span class="n" style="color: #333;">seqlen</span><span class="p">);</span></span>
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780
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838
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<pre style="margin: 0;"> <span id="LC838" class="line" lang="cpp"> <span class="n" style="color: #333;">GFREE</span><span class="p">(</span><span class="n" style="color: #333;">exont</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC839" class="line" lang="cpp"> <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">@@ -793,8 +851,6 @@ GTData::GTData(GffObj* t, GenomicSeqData* gd):rna(t),gdata(gd), locus(NULL), rep</td>
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851
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<pre style="margin: 0;"> <span id="LC851" 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="k" style="font-weight: 600;">this</span><span class="p">);</span></span>
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852
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<pre style="margin: 0;"> <span id="LC852" class="line" lang="cpp"><span class="p">}</span></span>
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853
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<pre style="margin: 0;"> <span id="LC853" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC796" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC797" class="line" lang="cpp"></span>
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854
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<pre style="margin: 0;"> <span id="LC854" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">GffLoader</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">unsplContained</span><span class="p">(</span><span class="n" style="color: #333;">GffObj</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">ti</span><span class="p">,</span> <span class="n" style="color: #333;">GffObj</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">tj</span><span class="p">)</span> <span class="p">{</span></span>
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799
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855
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<pre style="margin: 0;"> <span id="LC855" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//returns true only if ti (which MUST be single-exon) is "almost" contained in any of tj's exons</span></span>
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<pre style="margin: 0;"> <span id="LC856" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//but it does not cross any intron-exon boundary of tj</span></span>
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<a href="https://salsa.debian.org/med-team/gffread/-/compare/b60b67e61264f6b52333bdea38f528e59e0e08ce...852c8655e87bcaf4d8a1f48edb5d2f9ee6c682fb#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">@@ -19,7 +19,6 @@ extern FILE* f_y; //wrting fasta with translated CDS</td>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="objective_c"></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="objective_c"><span class="k" style="font-weight: 600;">extern</span> <span class="kt" style="color: #458; font-weight: 600;">FILE</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">f_j</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">//wrting junctions (introns)</span></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="objective_c"></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="objective_c"></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="objective_c"><span class="k" style="font-weight: 600;">extern</span> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">TFilters</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="objective_c"></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="objective_c"><span class="k" style="font-weight: 600;">extern</span> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">wfaNoCDS</span><span class="p">;</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -56,10 +55,6 @@ extern bool fullCDSonly; // starts with START, ends with STOP codon</td>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="objective_c"><span class="k" style="font-weight: 600;">extern</span> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">multiExon</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="objective_c"><span class="k" style="font-weight: 600;">extern</span> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">writeExonSegs</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="objective_c"><span class="k" style="font-weight: 600;">extern</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;">tracklabel</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="objective_c"><span class="k" style="font-weight: 600;">extern</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;">rfltGSeq</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="objective_c"><span class="k" style="font-weight: 600;">extern</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">rfltStrand</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="objective_c"><span class="k" style="font-weight: 600;">extern</span> <span class="n" style="color: #333;">uint</span> <span class="n" style="color: #333;">rfltStart</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="objective_c"><span class="k" style="font-weight: 600;">extern</span> <span class="n" style="color: #333;">uint</span> <span class="n" style="color: #333;">rfltEnd</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="objective_c"><span class="k" style="font-weight: 600;">extern</span> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">rfltWithin</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">//check for full containment within given range</span></span>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="objective_c"><span class="k" style="font-weight: 600;">extern</span> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">addDescr</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="objective_c"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -94,6 +89,10 @@ typedef bool GFValidateFunc(GffObj* gf);</td>
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<pre style="margin: 0;"> <span id="LC89" class="line" lang="objective_c"><span class="c1" style="color: #998; font-style: italic;">//keep/set original/old strand</span></span>
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="objective_c"><span class="cp" style="color: #999; font-weight: 600;">#define T_SET_OSTRAND(d, s) d |= s</span></span>
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="objective_c"></span>
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="objective_c"><span class="k" style="font-weight: 600;">extern</span> <span class="n" style="color: #333;">GRangeParser</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">fltRange</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="objective_c"></span>
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="objective_c"><span class="k" style="font-weight: 600;">extern</span> <span class="n" style="color: #333;">GRangeParser</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">fltJunction</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="objective_c"></span>
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<pre style="margin: 0;"> <span id="LC96" class="line" lang="objective_c"><span class="n" style="color: #333;">class</span> <span class="n" style="color: #333;">SeqInfo</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">//populated from the -s option of gffread</span></span>
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<pre style="margin: 0;"> <span id="LC97" class="line" lang="objective_c"> <span class="nl">public:</span></span>
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<pre style="margin: 0;"> <span id="LC98" class="line" lang="objective_c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">len</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="128" style="width: 35px; color: rgba(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">@@ -129,7 +128,6 @@ char* getSeqDescr(char* seqid);</td>
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129
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<pre style="margin: 0;"> <span id="LC128" class="line" lang="objective_c"><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="nf" style="color: #900; font-weight: 600;">getSeqName</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">seqid</span><span class="p">);</span></span>
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130
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129
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<pre style="margin: 0;"> <span id="LC129" class="line" lang="objective_c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">adjust_stopcodon</span><span class="p">(</span><span class="n" style="color: #333;">GffObj</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">gffrec</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">adj</span><span class="p">,</span> <span class="n" style="color: #333;">GList</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">GSeg</span><span class="o" style="font-weight: 600;">>*</span> <span class="n" style="color: #333;">seglst</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">NULL</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC130" class="line" lang="objective_c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">printTableData</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">FILE</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">f</span><span class="p">,</span> <span class="n" style="color: #333;">GffObj</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">g</span><span class="p">,</span> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">inFasta</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">false</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC132" class="line" lang="objective_c"><span class="n" style="color: #333;">bool</span> <span class="nf" style="color: #900; font-weight: 600;">process_transcript</span><span class="p">(</span><span class="n" style="color: #333;">GFastaDb</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">gfasta</span><span class="p">,</span> <span class="n" style="color: #333;">GffObj</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">gffrec</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC131" class="line" lang="objective_c"></span>
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<pre style="margin: 0;"> <span id="LC132" class="line" lang="objective_c"><span class="k" style="font-weight: 600;">enum</span> <span class="n" style="color: #333;">ETableFieldType</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC133" class="line" lang="objective_c"> <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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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -803,6 +801,8 @@ class GffLoader {</td>
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<pre style="margin: 0;"> <span id="LC801" class="line" lang="objective_c"> <span class="p">}</span></span>
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804
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<pre style="margin: 0;"> <span id="LC802" class="line" lang="objective_c"></span>
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<pre style="margin: 0;"> <span id="LC803" class="line" lang="objective_c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">validateGffRec</span><span class="p">(</span><span class="n" style="color: #333;">GffObj</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">gffrec</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC804" class="line" lang="objective_c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">process_transcript</span><span class="p">(</span><span class="n" style="color: #333;">GFastaDb</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">gfasta</span><span class="p">,</span> <span class="n" style="color: #333;">GffObj</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">gffrec</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC805" class="line" lang="objective_c"></span>
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<pre style="margin: 0;"> <span id="LC806" class="line" lang="objective_c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">checkFilters</span><span class="p">(</span><span class="n" style="color: #333;">GffObj</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">gffrec</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC807" class="line" lang="objective_c"></span>
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<pre style="margin: 0;"> <span id="LC808" class="line" lang="objective_c"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">collectIntrons</span><span class="p">(</span><span class="n" style="color: #333;">GffObj</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">t</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">//for -j output</span></span>
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<a href="https://salsa.debian.org/med-team/gffread/-/compare/b60b67e61264f6b52333bdea38f528e59e0e08ce...852c8655e87bcaf4d8a1f48edb5d2f9ee6c682fb#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">@@ -4,13 +4,14 @@</td>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#define __STDC_FORMAT_MACROS</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <inttypes.h></span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#define VERSION "0.12.<span class="idiff left right">4</span>"</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#define VERSION "0.12.<span class="idiff left right">7</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 [-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>] [-t <trackname>] [-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>] [-t <trackname>] [-r [<strand>]<chr>:<start>-<end> [-R]]\n\</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"> [--jmatch <chr>:<start>-<end>] [--no-pseudo] \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;"> [-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;"> [--ids <IDs.lst> | --nids <IDs.lst>] [--attrs <attr-list>] [-i <maxintron>]\n\</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"> <span class="idiff left right">[-j ]</span>[--ids <IDs.lst> | --nids <IDs.lst>] [--attrs <attr-list>] [-i <maxintron>]\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;"> [--stream] [--bed | --gtf | --tlf] [--table <attrlist>] [--sort-by <ref.lst>]\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;"> [<input_gff>] \n\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;"> Filter, convert or cluster GFF/GTF/BED records, extract the sequence of\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">@@ -20,14 +21,15 @@ gffread [-g <genomic_seqs_fasta> | <dir>] [-s <seq_info.fsize>] \n\</td>
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<pre style="margin: 0;"> <span id="LC21" 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="LC22" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"> \n\</span></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">Options:\n\</span></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"> -i discard transcripts having an intron larger than <maxintron>\n\</span></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"> --ids discard records/transcripts if their IDs are not listed in <IDs.lst>\n\</span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"> --nids discard records/transcripts if their IDs are listed in <IDs.lst>\n\</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"> -i discard transcripts having an intron larger than <maxintron>\n\</span></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"> -l discard transcripts shorter than <minlen> bases\n\</span></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"> -r only show transcripts overlapping coordinate range <start>..<end>\n\</span></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"> (on chromosome/contig <chr>, strand <strand> if provided)\n\</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"> -R for -r option, discard all transcripts that are not fully \n\</span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"> contained within the given range\n\</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"> --jmatch only output transcripts matching the given junction\n\</span></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"> -U discard single-exon transcripts\n\</span></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"> -C coding only: discard mRNAs that have no CDS features\n\</span></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"> --nc non-coding only: discard mRNAs that have CDS features\n\</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -105,14 +107,14 @@ Output options:\n\</td>
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<pre style="margin: 0;"> <span id="LC107" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"> -g full path to a multi-fasta file with the genomic sequences\n\</span></span>
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<pre style="margin: 0;"> <span id="LC108" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"> for all input mappings, OR a directory with single-fasta files\n\</span></span>
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<pre style="margin: 0;"> <span id="LC109" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"> (one per genomic sequence, with file names matching sequence names)\n\</span></span>
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<pre style="margin: 0;">-<span id="LC108" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"> -j <span class="idiff left right">write a tab delimited file with all the junctions (intron coordinates)</span>\n\</span></span>
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"> -j <span class="idiff left right">output the junctions and the corresponding transcripts</span>\n\</span></span>
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<pre style="margin: 0;"> <span id="LC111" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"> -w write a fasta file with spliced exons for each transcript\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;"> --w-add <N> for the -w option, extract additional <N> bases\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;"> both upstream and downstream of the transcript boundaries\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;"> --w-nocds for -w, disable the output of CDS info in the FASTA file\n\</span></span>
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113
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115
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<pre style="margin: 0;"> <span id="LC115" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"> -x write a fasta file with spliced CDS for each GFF transcript\n\</span></span>
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114
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116
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<pre style="margin: 0;"> <span id="LC116" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"> -y write a protein fasta file with the translation of CDS for each record\n\</span></span>
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115
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<pre style="margin: 0;">-<span id="LC115" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"> -W for -w and -<span class="idiff left right">x</span> options, write in the FASTA defline all the exon\n\</span></span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"> -W for -w<span class="idiff left">, -x</span> and -<span class="idiff right">y</span> options, write in the FASTA defline all the exon\n\</span></span>
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116
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118
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<pre style="margin: 0;"> <span id="LC118" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"> coordinates projected onto the spliced sequence;\n\</span></span>
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117
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119
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<pre style="margin: 0;"> <span id="LC119" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"> -S for -y option, use '*' instead of '.' as stop codon translation\n\</span></span>
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118
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120
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<pre style="margin: 0;"> <span id="LC120" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;"> -L Ensembl GTF to GFF3 conversion, adds version to IDs\n\</span></span>
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<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">@@ -252,11 +254,6 @@ void setTableFormat(GStr& s) {</td>
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252
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<pre style="margin: 0;"> <span id="LC254" 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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<pre style="margin: 0;"> <span id="LC255" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC256" class="line" lang="cpp"> <span class="p">}</span></span>
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255
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<pre style="margin: 0;">-<span id="LC255" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">w</span><span class="o" style="font-weight: 600;">==</span><span class="s" style="color: #d14;">"geneID"</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">w</span><span class="o" style="font-weight: 600;">==</span><span class="s" style="color: #d14;">"gene_id"</span><span class="p">)</span> <span class="p">{</span></span>
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256
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<pre style="margin: 0;">-<span id="LC256" class="line" lang="cpp"> <span class="n" style="color: #333;">CTableField</span> <span class="n" style="color: #333;">tcol</span><span class="p">(</span><span class="n" style="color: #333;">ctfGFF_geneID</span><span class="p">);</span></span>
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257
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<pre style="margin: 0;">-<span id="LC257" 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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258
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<pre style="margin: 0;">-<span id="LC258" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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259
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<pre style="margin: 0;">-<span id="LC259" class="line" lang="cpp"> <span class="p">}</span></span>
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257
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<pre style="margin: 0;"> <span id="LC257" 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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261
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258
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<pre style="margin: 0;"> <span id="LC258" 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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<pre style="margin: 0;"> <span id="LC259" class="line" lang="cpp"> <span class="n" style="color: #333;">tableCols</span><span class="p">.</span><span class="n" style="color: #333;">Add</span><span class="p">(</span><span class="n" style="color: #333;">tcol</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="392" style="width: 35px; color: rgba(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="389" style="width: 35px; color: rgba(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">@@ -392,7 +389,8 @@ void shutDown() {</td>
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392
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389
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<pre style="margin: 0;"> <span id="LC389" class="line" lang="cpp"> <span class="n" style="color: #333;">seqinfo</span><span class="p">.</span><span class="n" style="color: #333;">Clear</span><span class="p">();</span></span>
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393
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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;">//if (faseq!=NULL) delete faseq;</span></span>
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394
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391
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<pre style="margin: 0;"> <span id="LC391" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//if (gcdb!=NULL) delete gcdb;</span></span>
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395
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<pre style="margin: 0;">-<span id="LC395" class="line" lang="cpp"> <span class="n" style="color: #333;">GFREE</span><span class="p">(</span><span class="n" style="color: #333;">rfltGSeq</span><span class="p">);</span></span>
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392
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<pre style="margin: 0;">+<span id="LC392" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">delete</span> <span class="n" style="color: #333;">fltRange</span><span class="p">;</span></span>
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393
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<pre style="margin: 0;">+<span id="LC393" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">delete</span> <span class="n" style="color: #333;">fltJunction</span><span class="p">;</span></span>
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394
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<pre style="margin: 0;"> <span id="LC394" class="line" lang="cpp"> <span class="n" style="color: #333;">FWCLOSE</span><span class="p">(</span><span class="n" style="color: #333;">f_out</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;">FWCLOSE</span><span class="p">(</span><span class="n" style="color: #333;">f_w</span><span class="p">);</span></span>
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398
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396
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<pre style="margin: 0;"> <span id="LC396" class="line" lang="cpp"> <span class="n" style="color: #333;">FWCLOSE</span><span class="p">(</span><span class="n" style="color: #333;">f_x</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="403" style="width: 35px; color: rgba(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="401" style="width: 35px; color: rgba(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">@@ -403,11 +401,15 @@ void shutDown() {</td>
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<pre style="margin: 0;"> <span id="LC401" 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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<pre style="margin: 0;"> <span id="LC402" class="line" lang="cpp"> <span class="n" style="color: #333;">GArgs</span> <span class="n" style="color: #333;">args</span><span class="p">(</span><span class="n" style="color: #333;">argc</span><span class="p">,</span> <span class="n" style="color: #333;">argv</span><span class="p">,</span></span>
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405
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403
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<pre style="margin: 0;"> <span id="LC403" class="line" lang="cpp"> <span class="s" style="color: #d14;">"version;debug;merge;stream;adj-stop;bed;in-bed;tlf;in-tlf;cluster-only;nc;cov-info;help;"</span></span>
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406
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<pre style="margin: 0;">-<span id="LC406" class="line" lang="cpp"> <span class="s" style="color: #d14;">"sort-alpha;keep-genes;w-nocds;attrs=;w-add=;ids=;nids=<span class="idiff left right">0</span>;gtf;keep-comments;keep-exon-attrs;force-exons;t-adopt;gene2exon;"</span></span>
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404
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<pre style="margin: 0;">+<span id="LC404" class="line" lang="cpp"> <span class="s" style="color: #d14;">"sort-alpha;keep-genes;w-nocds;attrs=;w-add=;ids=;nids=<span class="idiff left right">;jmatch=</span>;gtf;keep-comments;keep-exon-attrs;force-exons;t-adopt;gene2exon;"</span></span>
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407
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405
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<pre style="margin: 0;"> <span id="LC405" class="line" lang="cpp"> <span class="s" style="color: #d14;">"ignore-locus;no-pseudo;table=sort-by=hvOUNHPWCVJMKQYTDARSZFGLEBm:g:i:r:s:l:t:o:w:x:y:j:d:"</span><span class="p">);</span></span>
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408
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406
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<pre style="margin: 0;"> <span id="LC406" 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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409
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407
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<pre style="margin: 0;"> <span id="LC407" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">numfiles</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">startNonOpt</span><span class="p">();</span></span>
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410
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<pre style="margin: 0;">-<span id="LC410" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">getOpt</span><span class="p">(</span><span class="sc" style="color: #d14;">'h'</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">getOpt</span><span class="p">(</span><span class="s" style="color: #d14;">"help"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span> <span class="n" style="color: #333;">numfiles</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">hasStdInput</span><span class="p">()))</span> <span class="p">{</span></span>
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408
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<pre style="margin: 0;">+<span id="LC408" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">getOpt</span><span class="p">(</span><span class="s" style="color: #d14;">"version"</span><span class="p">))</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC409" class="line" lang="cpp"> <span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="n" style="color: #333;">VERSION</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC410" class="line" lang="cpp"> <span class="n" style="color: #333;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC411" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC412" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">getOpt</span><span class="p">(</span><span class="sc" style="color: #d14;">'h'</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">getOpt</span><span class="p">(</span><span class="s" style="color: #d14;">"help"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span> <span class="n" style="color: #333;">numfiles</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">haveStdInput</span><span class="p">()))</span> <span class="p">{</span></span>
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411
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413
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<pre style="margin: 0;"> <span id="LC413" 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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412
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414
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<pre style="margin: 0;"> <span id="LC414" class="line" lang="cpp"> <span class="n" style="color: #333;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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413
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415
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<pre style="margin: 0;"> <span id="LC415" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="491" style="width: 35px; color: rgba(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="493" style="width: 35px; color: rgba(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">@@ -491,10 +493,6 @@ int main(int argc, char* argv[]) {</td>
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491
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493
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<pre style="margin: 0;"> <span id="LC493" class="line" lang="cpp"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"Command line was:</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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492
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494
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<pre style="margin: 0;"> <span id="LC494" class="line" lang="cpp"> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">printCmdLine</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">);</span></span>
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493
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495
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<pre style="margin: 0;"> <span id="LC495" class="line" lang="cpp"> <span class="p">}</span></span>
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494
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<pre style="margin: 0;">-<span id="LC494" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">getOpt</span><span class="p">(</span><span class="s" style="color: #d14;">"version"</span><span class="p">))</span> <span class="p">{</span></span>
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495
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<pre style="margin: 0;">-<span id="LC495" class="line" lang="cpp"> <span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="n" style="color: #333;">VERSION</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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496
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<pre style="margin: 0;">-<span id="LC496" class="line" lang="cpp"> <span class="n" style="color: #333;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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497
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<pre style="margin: 0;">-<span id="LC497" class="line" lang="cpp"> <span class="p">}</span></span>
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498
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496
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<pre style="margin: 0;"> <span id="LC496" class="line" lang="cpp"> <span class="n" style="color: #333;">gffloader</span><span class="p">.</span><span class="n" style="color: #333;">fullAttributes</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">getOpt</span><span class="p">(</span><span class="sc" style="color: #d14;">'F'</span><span class="p">)</span><span class="o" style="font-weight: 600;">!=</span><span class="nb" style="color: #0086b3;">NULL</span><span class="p">);</span></span>
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499
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497
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<pre style="margin: 0;"> <span id="LC497" class="line" lang="cpp"> <span class="n" style="color: #333;">gffloader</span><span class="p">.</span><span class="n" style="color: #333;">keep_AllExonAttrs</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-exon-attrs"</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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498
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<pre style="margin: 0;"> <span id="LC498" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">gffloader</span><span class="p">.</span><span class="n" style="color: #333;">keep_AllExonAttrs</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">gffloader</span><span class="p">.</span><span class="n" style="color: #333;">fullAttributes</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="558" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="556" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -558,44 +556,22 @@ int main(int argc, char* argv[]) {</td>
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558
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556
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<pre style="margin: 0;"> <span id="LC556" class="line" lang="cpp"> <span class="n" style="color: #333;">gffloader</span><span class="p">.</span><span class="n" style="color: #333;">fullAttributes</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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559
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557
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<pre style="margin: 0;"> <span id="LC557" class="line" lang="cpp"> <span class="p">}</span></span>
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560
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558
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<pre style="margin: 0;"> <span id="LC558" class="line" lang="cpp"> <span class="n" style="color: #333;">rfltWithin</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">getOpt</span><span class="p">(</span><span class="sc" style="color: #d14;">'R'</span><span class="p">)</span><span class="o" style="font-weight: 600;">!=</span><span class="nb" style="color: #0086b3;">NULL</span><span class="p">);</span></span>
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561
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<pre style="margin: 0;">-<span id="LC561" class="line" lang="cpp"> <span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">getOpt</span><span class="p">(</span><span class="sc" style="color: #d14;">'r'</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC562" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">is_empty</span><span class="p">())</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC563" class="line" lang="cpp"> <span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">trim</span><span class="p">();</span></span>
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564
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<pre style="margin: 0;">-<span id="LC564" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span><span class="o" style="font-weight: 600;">==</span><span class="sc" style="color: #d14;">'+'</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">s</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span><span class="o" style="font-weight: 600;">==</span><span class="sc" style="color: #d14;">'-'</span><span class="p">)</span> <span class="p">{</span></span>
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565
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<pre style="margin: 0;">-<span id="LC565" class="line" lang="cpp"> <span class="n" style="color: #333;">rfltStrand</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">s</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></span>
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<pre style="margin: 0;">-<span id="LC566" class="line" lang="cpp"> <span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">cut</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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567
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<pre style="margin: 0;">-<span id="LC567" class="line" lang="cpp"> <span class="p">}</span></span>
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568
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<pre style="margin: 0;">-<span id="LC568" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">isep</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;">index</span><span class="p">(</span><span class="sc" style="color: #d14;">':'</span><span class="p">);</span></span>
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569
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<pre style="margin: 0;">-<span id="LC569" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">isep</span><span class="o" style="font-weight: 600;">></span><span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;">//gseq name given</span></span>
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570
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<pre style="margin: 0;">-<span id="LC570" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">rfltStrand</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="p">(</span><span class="n" style="color: #333;">s</span><span class="p">[</span><span class="n" style="color: #333;">isep</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">==</span><span class="sc" style="color: #d14;">'+'</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">s</span><span class="p">[</span><span class="n" style="color: #333;">isep</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">==</span><span class="sc" style="color: #d14;">'-'</span><span class="p">))</span> <span class="p">{</span></span>
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571
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<pre style="margin: 0;">-<span id="LC571" class="line" lang="cpp"> <span class="n" style="color: #333;">isep</span><span class="o" style="font-weight: 600;">--</span><span class="p">;</span></span>
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572
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<pre style="margin: 0;">-<span id="LC572" class="line" lang="cpp"> <span class="n" style="color: #333;">rfltStrand</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;">isep</span><span class="p">];</span></span>
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573
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<pre style="margin: 0;">-<span id="LC573" class="line" lang="cpp"> <span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">cut</span><span class="p">(</span><span class="n" style="color: #333;">isep</span><span class="p">,</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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574
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<pre style="margin: 0;">-<span id="LC574" class="line" lang="cpp"> <span class="p">}</span></span>
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575
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<pre style="margin: 0;">-<span id="LC575" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">isep</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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576
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<pre style="margin: 0;">-<span id="LC576" class="line" lang="cpp"> <span class="n" style="color: #333;">rfltGSeq</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">Gstrdup</span><span class="p">((</span><span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">substr</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="n" style="color: #333;">isep</span><span class="p">)).</span><span class="n" style="color: #333;">chars</span><span class="p">());</span></span>
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577
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<pre style="margin: 0;">-<span id="LC577" class="line" lang="cpp"> <span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">cut</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="n" style="color: #333;">isep</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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578
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<pre style="margin: 0;">-<span id="LC578" class="line" lang="cpp"> <span class="p">}</span></span>
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579
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<pre style="margin: 0;">-<span id="LC579" class="line" lang="cpp"> <span class="n" style="color: #333;">GStr</span> <span class="n" style="color: #333;">gsend</span><span class="p">;</span></span>
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580
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<pre style="margin: 0;">-<span id="LC580" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">slast</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;">s</span><span class="p">.</span><span class="n" style="color: #333;">length</span><span class="p">()</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">];</span></span>
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581
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<pre style="margin: 0;">-<span id="LC581" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">rfltStrand</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="p">(</span><span class="n" style="color: #333;">slast</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;">slast</span><span class="o" style="font-weight: 600;">==</span><span class="sc" style="color: #d14;">'-'</span><span class="p">))</span> <span class="p">{</span></span>
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582
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<pre style="margin: 0;">-<span id="LC582" class="line" lang="cpp"> <span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">chomp</span><span class="p">(</span><span class="n" style="color: #333;">slast</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC583" class="line" lang="cpp"> <span class="n" style="color: #333;">rfltStrand</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">slast</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC584" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC585" 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;">index</span><span class="p">(</span><span class="s" style="color: #d14;">".."</span><span class="p">)</span><span class="o" style="font-weight: 600;">>=</span><span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="n" style="color: #333;">gsend</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;">split</span><span class="p">(</span><span class="s" style="color: #d14;">".."</span><span class="p">);</span></span>
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586
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<pre style="margin: 0;">-<span id="LC586" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">gsend</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;">split</span><span class="p">(</span><span class="sc" style="color: #d14;">'-'</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC587" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">is_empty</span><span class="p">())</span> <span class="n" style="color: #333;">rfltStart</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="n" style="color: #333;">uint</span><span class="p">)</span><span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">asInt</span><span class="p">();</span></span>
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<pre style="margin: 0;">-<span id="LC588" 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;">gsend</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="LC589" class="line" lang="cpp"> <span class="n" style="color: #333;">rfltEnd</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="n" style="color: #333;">uint</span><span class="p">)</span><span class="n" style="color: #333;">gsend</span><span class="p">.</span><span class="n" style="color: #333;">asInt</span><span class="p">();</span></span>
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590
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<pre style="margin: 0;">-<span id="LC590" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">rfltEnd</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;">rfltEnd</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">MAX_UINT</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC591" class="line" lang="cpp"> <span class="p">}</span></span>
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592
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<pre style="margin: 0;">-<span id="LC592" class="line" lang="cpp"> <span class="p">}</span> <span class="c1" style="color: #998; font-style: italic;">//gseq/range filtering</span></span>
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593
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<pre style="margin: 0;">-<span id="LC593" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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559
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<pre style="margin: 0;">+<span id="LC559" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">sz</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">getOpt</span><span class="p">(</span><span class="sc" style="color: #d14;">'r'</span><span class="p">);</span></span>
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560
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<pre style="margin: 0;">+<span id="LC560" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">sz</span><span class="p">)</span> <span class="p">{</span></span>
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561
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<pre style="margin: 0;">+<span id="LC561" class="line" lang="cpp"> <span class="n" style="color: #333;">fltRange</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">GRangeParser</span><span class="p">(</span><span class="n" style="color: #333;">sz</span><span class="p">);</span></span>
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562
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<pre style="margin: 0;">+<span id="LC562" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">fltRange</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">end</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="c1" style="color: #998; font-style: italic;">//end coordinate not given</span></span>
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563
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<pre style="margin: 0;">+<span id="LC563" class="line" lang="cpp"> <span class="n" style="color: #333;">fltRange</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;">UINT_MAX</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC564" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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594
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565
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<pre style="margin: 0;"> <span id="LC565" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">rfltWithin</span><span class="p">)</span></span>
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595
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566
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<pre style="margin: 0;"> <span id="LC566" class="line" lang="cpp"> <span class="n" style="color: #333;">GError</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: option -R requires -r!</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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596
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<pre style="margin: 0;">-<span id="LC596" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//if (rfltWholeTranscript)</span></span>
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<pre style="margin: 0;">-<span id="LC597" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// GError("Error: option -P requires -r!\n");</span></span>
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<pre style="margin: 0;">-<span id="LC598" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC567" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC568" class="line" lang="cpp"> <span class="n" style="color: #333;">sz</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;">"jmatch"</span><span class="p">);</span></span>
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569
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<pre style="margin: 0;">+<span id="LC569" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">sz</span><span class="p">)</span> <span class="p">{</span></span>
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570
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<pre style="margin: 0;">+<span id="LC570" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//TODO: check if this is a file?</span></span>
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571
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<pre style="margin: 0;">+<span id="LC571" class="line" lang="cpp"> <span class="n" style="color: #333;">fltJunction</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">GRangeParser</span><span class="p">(</span><span class="n" style="color: #333;">sz</span><span class="p">);</span></span>
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572
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<pre style="margin: 0;">+<span id="LC572" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">fltJunction</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="p">)</span> <span class="n" style="color: #333;">fltJunction</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="mi" style="color: #099;">0</span><span class="p">;</span></span>
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573
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<pre style="margin: 0;">+<span id="LC573" class="line" lang="cpp"> <span class="p">}</span> <span class="c1" style="color: #998; font-style: italic;">//gseq/range filtering</span></span>
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574
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<pre style="margin: 0;">+<span id="LC574" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC575" class="line" lang="cpp"> <span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">getOpt</span><span class="p">(</span><span class="sc" style="color: #d14;">'m'</span><span class="p">);</span></span>
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600
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576
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<pre style="margin: 0;"> <span id="LC576" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">is_empty</span><span class="p">())</span> <span class="p">{</span></span>
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601
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577
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<pre style="margin: 0;"> <span id="LC577" 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;">ft</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">fopen</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">,</span><span class="s" style="color: #d14;">"r"</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="645" style="width: 35px; color: rgba(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="621" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -645,7 +621,7 @@ int main(int argc, char* argv[]) {</td>
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645
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621
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<pre style="margin: 0;"> <span id="LC621" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">f_w</span><span class="o" style="font-weight: 600;">!=</span><span class="nb" style="color: #0086b3;">NULL</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">getOpt</span><span class="p">(</span><span class="s" style="color: #d14;">"w-nocds"</span><span class="p">))</span></span>
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646
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622
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<pre style="margin: 0;"> <span id="LC622" class="line" lang="cpp"> <span class="n" style="color: #333;">wfaNoCDS</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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647
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623
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<pre style="margin: 0;"> <span id="LC623" class="line" lang="cpp"></span>
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648
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<pre style="margin: 0;">-<span id="LC648" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">f_out</span><span class="o" style="font-weight: 600;">==</span><span class="nb" style="color: #0086b3;">NULL</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">f_w</span><span class="o" style="font-weight: 600;">==</span><span class="nb" style="color: #0086b3;">NULL</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">f_x</span><span class="o" style="font-weight: 600;">==</span><span class="nb" style="color: #0086b3;">NULL</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">f_y</span><span class="o" style="font-weight: 600;">==</span><span class="nb" style="color: #0086b3;">NULL</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">covInfo</span><span class="p">)</span></span>
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624
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<pre style="margin: 0;">+<span id="LC624" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">f_out</span><span class="o" style="font-weight: 600;">==</span><span class="nb" style="color: #0086b3;">NULL</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">f_w</span><span class="o" style="font-weight: 600;">==</span><span class="nb" style="color: #0086b3;">NULL</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">f_x</span><span class="o" style="font-weight: 600;">==</span><span class="nb" style="color: #0086b3;">NULL</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">f_y</span><span class="o" style="font-weight: 600;">==</span><span class="nb" style="color: #0086b3;">NULL</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;"><span class="idiff left">f_j</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="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff right"> </span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">covInfo</span><span class="p">)</span></span>
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649
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625
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<pre style="margin: 0;"> <span id="LC625" 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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<pre style="margin: 0;"> <span id="LC626" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC627" 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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<a href="https://salsa.debian.org/med-team/gffread/-/compare/b60b67e61264f6b52333bdea38f528e59e0e08ce...852c8655e87bcaf4d8a1f48edb5d2f9ee6c682fb#ad76bfab75291d38945f9d9d0587235d3770a87c"><strong>prep_source.sh</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -14,7 +14,7 @@ libdir=$pack/gclib/</td>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="shell"><span class="s2" style="color: #d14;">cp LICENSE README.md gffread.cpp gff_utils.{h,cpp} </span><span class="nv" style="color: #008080;">$pack</span><span class="s2" style="color: #d14;">/</span></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="shell"><span class="s2" style="color: #d14;">sed 's|</span><span class="se" style="color: #d14;">\.\.</span><span class="s2" style="color: #d14;">/gclib|./gclib|' Makefile > </span><span class="nv" style="color: #008080;">$pack</span><span class="s2" style="color: #d14;">/Makefile</span></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="shell"><span class="s2" style="color: #d14;">cp ../gclib/{GVec,GList,GHashMap,khashl}.hh ../gclib/xxhash.h </span><span class="nv" style="color: #008080;">$libdir</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="shell"><span class="s2" style="color: #d14;">cp ../gclib/{GVec,GList,GHashMap,khashl}.hh ../gclib/xxhash.h <span class="idiff left right">../gclib/wyhash.h ../gclib/GBitVec.h </span></span><span class="nv" style="color: #008080;">$libdir</span></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="shell"><span class="s2" style="color: #d14;">cp ../gclib/{GArgs,GBase,gdna,GStr,gff,codons,GFaSeqGet,GFastaIndex}.{h,cpp} </span><span class="nv" style="color: #008080;">$libdir</span></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="shell"><span class="s2" style="color: #d14;">tar cvfz </span><span class="nv" style="color: #008080;">$pack</span><span class="s2" style="color: #d14;">.tar.gz </span><span class="nv" style="color: #008080;">$pack</span></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="shell"><span class="s2" style="color: #d14;">ls -l </span><span class="nv" style="color: #008080;">$pack</span><span class="s2" style="color: #d14;">.tar.gz</span></span>
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