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<h3>
Nilesh Patra pushed to branch master
at <a href="https://salsa.debian.org/med-team/gmap">Debian Med / gmap</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/gmap/-/commit/0c0c4b2ce0fe560fdfb34ff731e939d4d9555b35">0c0c4b2c</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-10-21T11:16:26+05:30</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/gmap/-/commit/91beb530ff3767d77a566ef84773dd8292dddbb7">91beb530</a></strong>
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<span>by Nilesh Patra</span>
<i>at 2020-10-21T11:16:27+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2020-10-14+ds</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/gmap/-/commit/c571e84af559f96795cc35227d474d95ae9df6e2">c571e84a</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-10-21T11:16:39+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/2020-10-14+ds'
Update to upstream version '2020-10-14+ds'
with Debian dir 21698ca0308be32dda7b7cc3e3ea65fae0b34395</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/gmap/-/commit/c42803c614bca47c818ce65af0a53b368a57e334">c42803c6</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-10-21T11:17:19+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Ready to upload to unstable
</pre>
</li>
</ul>
<h4>11 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#00fe7828d56d7a3ee4030d6cea057cf13f50e70c">
ChangeLog
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<li class="file-stats">
<a href="#b33892fbddeffc3368077b4904ad0b3d562a7312">
VERSION
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<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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</li>
<li class="file-stats">
<a href="#e898dcb4575afbe2011dd3239a76d23e692b995d">
src/distant-rna.c
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</li>
<li class="file-stats">
<a href="#49786cab443f0fbab3b5bb48f2f310040d725d74">
src/genome128_hr.c
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<li class="file-stats">
<a href="#d747f527041a6e797f86fcd6f1fcd1562bab24a2">
src/gmap.c
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<li class="file-stats">
<a href="#c98399a907bb515fa302e9111b148f9f0da3c8ba">
src/kmer-search.c
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<li class="file-stats">
<a href="#667933d29731aaedc5d4c17a05fe5bbc8d9cc3ef">
src/pair.c
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<li class="file-stats">
<a href="#d6ba69bc1ae89700307c00a3b1afeef776cfb00a">
src/pair.h
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<li class="file-stats">
<a href="#2d331dd15dccff926559b191048c3a7d2d3a5fae">
src/stage3hr.c
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<li class="file-stats">
<a href="#aeb285890115a453e6448fd7de6fc67bf8daf3a4">
src/substring.c
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</li>
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<h4>Changes:</h4>
<li id="00fe7828d56d7a3ee4030d6cea057cf13f50e70c">
<a href="https://salsa.debian.org/med-team/gmap/-/compare/e36c478dd913ea44b8ccff832e1ed3c2409790ca...c42803c614bca47c818ce65af0a53b368a57e334#00fe7828d56d7a3ee4030d6cea057cf13f50e70c"><strong>ChangeLog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="">2020-10-15 twu</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang=""></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang=""> * VERSION, index.html: Updated version number</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang=""></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang=""> * gmap.c: Added option --nomargin. Removed -N abbreviation for --nolengths</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang=""></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang=""> * pair.c, pair.h: Fixed printing of ruler for long wrap lengths</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang=""></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang=""> * kmer-search.c: Fixed parameters to Genome_count_mismatches_substring and</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang=""> Substring_new in single_hits_gminus. Simplified indentation in</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang=""> search_transcriptome_ends</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang=""></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="">2020-10-14 twu</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang=""></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang=""> * stage3hr.c: Changed remap_transcriptome_p into a macro</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang=""></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang=""> * genome128_hr.c: Added assertions that pos5 < pos3</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang=""></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang=""> * distant-rna.c: Ensuring that pos5 < pos3 when checking for mismatches</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang=""></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang=""> * substring.c: Checking for pos3 == pos5 and not computing mismatches for</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang=""> that case</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang=""></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="">2020-10-13 twu</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang=""></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang=""> * kmer-search.c: Initializing abortp in the correct place for</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang=""> transcriptome-guided genomic alignment</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang=""></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="">2020-10-12 twu</span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang=""></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang=""> * fa_coords.pl.in: Checking for circular and altscaffold arguments to be</span>
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<a href="https://salsa.debian.org/med-team/gmap/-/compare/e36c478dd913ea44b8ccff832e1ed3c2409790ca...c42803c614bca47c818ce65af0a53b368a57e334#b33892fbddeffc3368077b4904ad0b3d562a7312"><strong>VERSION</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">2020-10-12</span></pre>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">2020-10-14</span></pre>
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<a href="https://salsa.debian.org/med-team/gmap/-/compare/e36c478dd913ea44b8ccff832e1ed3c2409790ca...c42803c614bca47c818ce65af0a53b368a57e334#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">gmap (2020-10-14+ds-1) unstable; 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"> * Team upload.</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"></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> -- Nilesh Patra <npatra974@gmail.com> Wed, 21 Oct 2020 11:17:19 +0530</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">gmap (2020-10-12+ds-1) unstable; urgency=medium</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"> * Team upload.</span>
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<a href="https://salsa.debian.org/med-team/gmap/-/compare/e36c478dd913ea44b8ccff832e1ed3c2409790ca...c42803c614bca47c818ce65af0a53b368a57e334#e898dcb4575afbe2011dd3239a76d23e692b995d"><strong>src/distant-rna.c</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">rcsid</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"$Id: distant-rna.c 223<span class="idiff left right">081 2020-09-13 14:21:03</span>Z twu $"</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">rcsid</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"$Id: distant-rna.c 223<span class="idiff left right">174 2020-10-15 01:50:42</span>Z twu $"</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifdef HAVE_CONFIG_H</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <config.h></span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -35,7 +35,7 @@ static char rcsid[] = "$Id: distant-rna.c 223081 2020-09-13 14:21:03Z twu $";</td>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/* For transcript splicing, need to increase MAXCHIMERAPATHS */</span></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/* #define MAXCHIMERAPATHS 100 */</span></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define MAXCHIMERAPATHS 10000</span></span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define MIN_SPLICE_EXON_LENGTH <span class="idiff left right">0</span></span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define MIN_SPLICE_EXON_LENGTH <span class="idiff left">1 </span></span><span class="cm" style="color: #998; font-style: italic;"><span class="idiff right">/* Needs to be greater than 0 */</span></span></span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define MIN_FRAGLENGTH 25</span></span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="n" style="color: #333;">Univ_IIT_T</span> <span class="n" style="color: #333;">chromosome_iit</span><span class="p">;</span></span>
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<li id="49786cab443f0fbab3b5bb48f2f310040d725d74">
<a href="https://salsa.debian.org/med-team/gmap/-/compare/e36c478dd913ea44b8ccff832e1ed3c2409790ca...c42803c614bca47c818ce65af0a53b368a57e334#49786cab443f0fbab3b5bb48f2f310040d725d74"><strong>src/genome128_hr.c</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">rcsid</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"$Id: genome128_hr.c 22<span class="idiff left right">2927 2020-06-29 16:07:54</span>Z twu $"</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">rcsid</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"$Id: genome128_hr.c 22<span class="idiff left right">3175 2020-10-15 01:50:58</span>Z twu $"</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifdef HAVE_CONFIG_H</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <config.h></span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -478,10 +478,8 @@ print_blocks_alt (Genomecomp_T *blocks, Genomecomp_T *alt_blocks, Univcoord_T st</td>
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478
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<pre style="margin: 0;"> <span id="LC478" class="line" lang="c"> <span class="n" style="color: #333;">Genomecomp_T</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">ref_ptr</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">snp_ptr</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC479" class="line" lang="c"> <span class="n" style="color: #333;">Univcoord_T</span> <span class="n" style="color: #333;">startblocki</span><span class="p">,</span> <span class="n" style="color: #333;">endblocki</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC480" class="line" lang="c"> <span class="n" style="color: #333;">Genomecomp_T</span> <span class="n" style="color: #333;">high</span><span class="p">,</span> <span class="n" style="color: #333;">low</span><span class="p">,</span> <span class="n" style="color: #333;">flags</span><span class="p">,</span> <span class="n" style="color: #333;">snpmask</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC481" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#if defined(WORDS_BIGENDIAN) || !defined(HAVE_SSE2)</span></span>
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<pre style="margin: 0;"> <span id="LC481" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">startcolumni</span><span class="p">,</span> <span class="n" style="color: #333;">endcolumni</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC482" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">startdiscard32</span><span class="p">,</span> <span class="n" style="color: #333;">enddiscard32</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC484" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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<pre style="margin: 0;"> <span id="LC483" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC484" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* sequence = (char *) CALLOC(length+1,sizeof(char)); */</span></span>
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<pre style="margin: 0;"> <span id="LC485" class="line" lang="c"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -492,6 +490,9 @@ print_blocks_alt (Genomecomp_T *blocks, Genomecomp_T *alt_blocks, Univcoord_T st</td>
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<pre style="margin: 0;"> <span id="LC490" class="line" lang="c"> <span class="n" style="color: #333;">endcolumni</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">endpos</span> <span class="o" style="font-weight: 600;">%</span> <span class="mi" style="color: #099;">128</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="mi" style="color: #099;">32</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC491" class="line" lang="c"> <span class="n" style="color: #333;">endblocki</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">endpos</span><span class="o" style="font-weight: 600;">/</span><span class="mi" style="color: #099;">128U</span><span class="o" style="font-weight: 600;">*</span><span class="mi" style="color: #099;">12</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">endcolumni</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC492" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#else</span></span>
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<pre style="margin: 0;">+<span id="LC493" class="line" lang="c"> <span class="n" style="color: #333;">startcolumni</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">startpos</span> <span class="o" style="font-weight: 600;">%</span> <span class="mi" style="color: #099;">128</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="mi" style="color: #099;">32</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC494" class="line" lang="c"> <span class="n" style="color: #333;">endcolumni</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">endpos</span> <span class="o" style="font-weight: 600;">%</span> <span class="mi" style="color: #099;">128</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="mi" style="color: #099;">32</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC495" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC496" class="line" lang="c"> <span class="n" style="color: #333;">startblocki</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">startpos</span><span class="o" style="font-weight: 600;">/</span><span class="mi" style="color: #099;">128U</span><span class="o" style="font-weight: 600;">*</span><span class="mi" style="color: #099;">12</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC497" class="line" lang="c"> <span class="n" style="color: #333;">endblocki</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">endpos</span><span class="o" style="font-weight: 600;">/</span><span class="mi" style="color: #099;">128U</span><span class="o" style="font-weight: 600;">*</span><span class="mi" style="color: #099;">12</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC498" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -5006,6 +5007,8 @@ int</td>
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<pre style="margin: 0;"> <span id="LC5007" class="line" lang="c"><span class="nf" style="color: #900; font-weight: 600;">Genome_count_mismatches_substring</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">ref_mismatches</span><span class="p">,</span> <span class="n" style="color: #333;">Genome_T</span> <span class="n" style="color: #333;">ome</span><span class="p">,</span> <span class="n" style="color: #333;">Genome_T</span> <span class="n" style="color: #333;">ome_alt</span><span class="p">,</span> <span class="n" style="color: #333;">Compress_T</span> <span class="n" style="color: #333;">query_compress</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC5008" class="line" lang="c"> <span class="n" style="color: #333;">Univcoord_T</span> <span class="n" style="color: #333;">left</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">pos5</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">pos3</span><span class="p">,</span> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">plusp</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">genestrand</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC5009" class="line" lang="c"></span>
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5010
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<pre style="margin: 0;">+<span id="LC5010" class="line" lang="c"> <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">pos5</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">pos3</span><span class="p">);</span></span>
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5011
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<pre style="margin: 0;">+<span id="LC5011" class="line" lang="c"></span>
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5009
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5012
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<pre style="margin: 0;"> <span id="LC5012" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">alt_blocks</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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5010
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5013
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<pre style="margin: 0;"> <span id="LC5013" class="line" lang="c"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">ref_mismatches</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Genome_count_mismatches_substring_ref</span><span class="p">(</span><span class="n" style="color: #333;">ome</span><span class="p">,</span><span class="n" style="color: #333;">query_compress</span><span class="p">,</span><span class="n" style="color: #333;">left</span><span class="p">,</span><span class="n" style="color: #333;">pos5</span><span class="p">,</span><span class="n" style="color: #333;">pos3</span><span class="p">,</span><span class="n" style="color: #333;">plusp</span><span class="p">,</span><span class="n" style="color: #333;">genestrand</span><span class="p">);</span></span>
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5011
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5014
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<pre style="margin: 0;"> <span id="LC5014" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">ref_mismatches</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="5695" style="width: 35px; color: rgba(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="5698" style="width: 35px; color: rgba(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">@@ -5695,6 +5698,8 @@ Genome_mismatches_left (int *mismatch_positions, int max_mismatches, Genome_T om</td>
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5695
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5698
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<pre style="margin: 0;"> <span id="LC5698" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span><span class="p">;</span></span>
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5696
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5699
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<pre style="margin: 0;"> <span id="LC5699" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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5697
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5700
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<pre style="margin: 0;"> <span id="LC5700" class="line" lang="c"></span>
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5701
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<pre style="margin: 0;">+<span id="LC5701" class="line" lang="c"> <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">pos5</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">pos3</span><span class="p">);</span></span>
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5702
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<pre style="margin: 0;">+<span id="LC5702" class="line" lang="c"></span>
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5698
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5703
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<pre style="margin: 0;"> <span id="LC5703" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">ome_alt</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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5699
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5704
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<pre style="margin: 0;"> <span id="LC5704" class="line" lang="c"> <span class="n" style="color: #333;">nmismatches</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mismatches_left</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">mismatch_positions</span><span class="p">),</span><span class="n" style="color: #333;">max_mismatches</span><span class="p">,</span><span class="n" style="color: #333;">ome</span><span class="p">,</span><span class="n" style="color: #333;">query_compress</span><span class="p">,</span></span>
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5700
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5705
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<pre style="margin: 0;"> <span id="LC5705" class="line" lang="c"> <span class="n" style="color: #333;">left</span><span class="p">,</span><span class="n" style="color: #333;">pos5</span><span class="p">,</span><span class="n" style="color: #333;">pos3</span><span class="p">,</span><span class="n" style="color: #333;">plusp</span><span class="p">,</span><span class="n" style="color: #333;">genestrand</span><span class="p">,</span><span class="n" style="color: #333;">query_unk_mismatch_p</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="5727" style="width: 35px; color: rgba(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="5732" style="width: 35px; color: rgba(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">@@ -5727,6 +5732,8 @@ Genome_mismatches_left_trim (int *mismatch_positions, int max_mismatches, Genome</td>
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5727
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5732
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<pre style="margin: 0;"> <span id="LC5732" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span><span class="p">;</span></span>
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5728
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5733
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<pre style="margin: 0;"> <span id="LC5733" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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5729
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5734
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<pre style="margin: 0;"> <span id="LC5734" class="line" lang="c"></span>
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5735
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<pre style="margin: 0;">+<span id="LC5735" class="line" lang="c"> <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">pos5</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">pos3</span><span class="p">);</span></span>
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5736
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<pre style="margin: 0;">+<span id="LC5736" class="line" lang="c"></span>
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5730
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5737
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<pre style="margin: 0;"> <span id="LC5737" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">ome_alt</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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5731
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5738
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<pre style="margin: 0;"> <span id="LC5738" class="line" lang="c"> <span class="n" style="color: #333;">nmismatches</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mismatches_left</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">mismatch_positions</span><span class="p">),</span><span class="n" style="color: #333;">max_mismatches</span><span class="p">,</span><span class="n" style="color: #333;">ome</span><span class="p">,</span><span class="n" style="color: #333;">query_compress</span><span class="p">,</span></span>
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5732
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5739
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<pre style="margin: 0;"> <span id="LC5739" class="line" lang="c"> <span class="n" style="color: #333;">left</span><span class="p">,</span><span class="n" style="color: #333;">pos5</span><span class="p">,</span><span class="n" style="color: #333;">pos3</span><span class="p">,</span><span class="n" style="color: #333;">plusp</span><span class="p">,</span><span class="n" style="color: #333;">genestrand</span><span class="p">,</span><span class="cm" style="color: #998; font-style: italic;">/*query_unk_mismatch_p*/</span><span class="nb" style="color: #0086b3;">false</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="6289" style="width: 35px; color: rgba(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">@@ -6282,6 +6289,8 @@ Genome_mismatches_right (int *mismatch_positions, int max_mismatches, Genome_T o</td>
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6282
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6289
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<pre style="margin: 0;"> <span id="LC6289" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span><span class="p">;</span></span>
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6283
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6290
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<pre style="margin: 0;"> <span id="LC6290" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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6284
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6291
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<pre style="margin: 0;"> <span id="LC6291" class="line" lang="c"></span>
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6292
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<pre style="margin: 0;">+<span id="LC6292" class="line" lang="c"> <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">pos5</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">pos3</span><span class="p">);</span></span>
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6293
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<pre style="margin: 0;">+<span id="LC6293" class="line" lang="c"></span>
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6285
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6294
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<pre style="margin: 0;"> <span id="LC6294" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">ome_alt</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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6286
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6295
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<pre style="margin: 0;"> <span id="LC6295" class="line" lang="c"> <span class="n" style="color: #333;">nmismatches</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mismatches_right</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">mismatch_positions</span><span class="p">),</span><span class="n" style="color: #333;">max_mismatches</span><span class="p">,</span><span class="n" style="color: #333;">ome</span><span class="p">,</span><span class="n" style="color: #333;">query_compress</span><span class="p">,</span></span>
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6287
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6296
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<pre style="margin: 0;"> <span id="LC6296" class="line" lang="c"> <span class="n" style="color: #333;">left</span><span class="p">,</span><span class="n" style="color: #333;">pos5</span><span class="p">,</span><span class="n" style="color: #333;">pos3</span><span class="p">,</span><span class="n" style="color: #333;">plusp</span><span class="p">,</span><span class="n" style="color: #333;">genestrand</span><span class="p">,</span><span class="n" style="color: #333;">query_unk_mismatch_p</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="6312" style="width: 35px; color: rgba(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="6321" style="width: 35px; color: rgba(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">@@ -6312,6 +6321,8 @@ Genome_mismatches_right_trim (int *mismatch_positions, int max_mismatches, Genom</td>
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6312
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6321
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<pre style="margin: 0;"> <span id="LC6321" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span><span class="p">;</span></span>
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6313
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6322
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<pre style="margin: 0;"> <span id="LC6322" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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6314
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6323
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<pre style="margin: 0;"> <span id="LC6323" class="line" lang="c"></span>
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6324
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<pre style="margin: 0;">+<span id="LC6324" class="line" lang="c"> <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">pos5</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">pos3</span><span class="p">);</span></span>
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6325
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<pre style="margin: 0;">+<span id="LC6325" class="line" lang="c"></span>
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6315
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6326
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<pre style="margin: 0;"> <span id="LC6326" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">ome_alt</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="6316" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6316
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6327
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<pre style="margin: 0;"> <span id="LC6327" class="line" lang="c"> <span class="n" style="color: #333;">nmismatches</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mismatches_right</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">mismatch_positions</span><span class="p">),</span><span class="n" style="color: #333;">max_mismatches</span><span class="p">,</span><span class="n" style="color: #333;">ome</span><span class="p">,</span><span class="n" style="color: #333;">query_compress</span><span class="p">,</span></span>
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<td class="diff-line-num old_line" data-linenumber="6317" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6317
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<td class="diff-line-num new_line" data-linenumber="6328" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6328
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<pre style="margin: 0;"> <span id="LC6328" class="line" lang="c"> <span class="n" style="color: #333;">left</span><span class="p">,</span><span class="n" style="color: #333;">pos5</span><span class="p">,</span><span class="n" style="color: #333;">pos3</span><span class="p">,</span><span class="n" style="color: #333;">plusp</span><span class="p">,</span><span class="n" style="color: #333;">genestrand</span><span class="p">,</span><span class="cm" style="color: #998; font-style: italic;">/*query_unk_mismatch_p*/</span><span class="nb" style="color: #0086b3;">false</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="6360" style="width: 35px; color: rgba(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="6371" style="width: 35px; color: rgba(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">@@ -6360,6 +6371,7 @@ Genome_first_kmer_left (int *nmismatches5, Genome_T ome, Compress_T query_compre</td>
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6360
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6371
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<pre style="margin: 0;"> <span id="LC6371" class="line" lang="c"> <span class="n" style="color: #333;">printf</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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6361
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6372
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<pre style="margin: 0;"> <span id="LC6372" class="line" lang="c"> <span class="p">);</span></span>
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6362
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6373
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<pre style="margin: 0;"> <span id="LC6373" class="line" lang="c"></span>
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6374
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<pre style="margin: 0;">+<span id="LC6374" class="line" lang="c"> <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">pos5</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">pos3</span><span class="p">);</span></span>
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6363
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6375
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<pre style="margin: 0;"> <span id="LC6375" class="line" lang="c"></span>
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6364
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6376
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<pre style="margin: 0;"> <span id="LC6376" class="line" lang="c"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">nmismatches5</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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6377
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<pre style="margin: 0;"> <span id="LC6377" class="line" lang="c"></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="6706" style="width: 35px; color: rgba(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">@@ -6694,6 +6706,8 @@ Genome_first_kmer_right (int *nmismatches3, Genome_T ome, Compress_T query_compr</td>
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6694
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6706
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<pre style="margin: 0;"> <span id="LC6706" class="line" lang="c"> <span class="n" style="color: #333;">printf</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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6707
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<pre style="margin: 0;"> <span id="LC6707" class="line" lang="c"> <span class="p">);</span></span>
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6696
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6708
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<pre style="margin: 0;"> <span id="LC6708" class="line" lang="c"></span>
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6709
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<pre style="margin: 0;">+<span id="LC6709" class="line" lang="c"> <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">pos5</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">pos3</span><span class="p">);</span></span>
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6710
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<pre style="margin: 0;">+<span id="LC6710" class="line" lang="c"></span>
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6711
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<pre style="margin: 0;"> <span id="LC6711" class="line" lang="c"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">nmismatches3</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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6698
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6712
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<pre style="margin: 0;"> <span id="LC6712" class="line" lang="c"></span>
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6699
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6713
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<pre style="margin: 0;"> <span id="LC6713" class="line" lang="c"> <span class="n" style="color: #333;">startblocki</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">left</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">pos5</span><span class="p">)</span><span class="o" style="font-weight: 600;">/</span><span class="mi" style="color: #099;">128U</span><span class="o" style="font-weight: 600;">*</span><span class="mi" style="color: #099;">12</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="7038" style="width: 35px; color: rgba(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">@@ -7024,6 +7038,7 @@ Genome_mark_mismatches_ref (char *genomic, int querylength, Compress_T query_com</td>
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7024
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7038
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<pre style="margin: 0;"> <span id="LC7038" class="line" lang="c"> <span class="n" style="color: #333;">printf</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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7025
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7039
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<pre style="margin: 0;"> <span id="LC7039" class="line" lang="c"> <span class="p">);</span></span>
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7026
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7040
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<pre style="margin: 0;"> <span id="LC7040" class="line" lang="c"></span>
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7041
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<pre style="margin: 0;">+<span id="LC7041" class="line" lang="c"> <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">pos5</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">pos3</span><span class="p">);</span></span>
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7027
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7042
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<pre style="margin: 0;"> <span id="LC7042" class="line" lang="c"></span>
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7028
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7043
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<pre style="margin: 0;"> <span id="LC7043" class="line" lang="c"> <span class="n" style="color: #333;">startblocki</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">left</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">pos5</span><span class="p">)</span><span class="o" style="font-weight: 600;">/</span><span class="mi" style="color: #099;">128U</span><span class="o" style="font-weight: 600;">*</span><span class="mi" style="color: #099;">12</span><span class="p">;</span></span>
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7029
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7044
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<pre style="margin: 0;"> <span id="LC7044" class="line" lang="c"> <span class="n" style="color: #333;">startcolumni</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">((</span><span class="n" style="color: #333;">left</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">pos5</span><span class="p">)</span> <span class="o" style="font-weight: 600;">%</span> <span class="mi" style="color: #099;">128</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="mi" style="color: #099;">32</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="7633" style="width: 35px; color: rgba(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">@@ -7618,6 +7633,8 @@ Genome_mark_mismatches (char *genomic, int querylength, Compress_T query_compres</td>
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7618
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7633
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<pre style="margin: 0;"> <span id="LC7633" class="line" lang="c"> <span class="n" style="color: #333;">Univcoord_T</span> <span class="n" style="color: #333;">left</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">pos5</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">pos3</span><span class="p">,</span></span>
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7619
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<td class="diff-line-num new_line" data-linenumber="7634" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7634
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<pre style="margin: 0;"> <span id="LC7634" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">plusp</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">genestrand</span><span class="p">)</span> <span class="p">{</span></span>
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7620
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7635
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<pre style="margin: 0;"> <span id="LC7635" class="line" lang="c"></span>
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7636
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<pre style="margin: 0;">+<span id="LC7636" class="line" lang="c"> <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">pos5</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">pos3</span><span class="p">);</span></span>
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7637
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<pre style="margin: 0;">+<span id="LC7637" class="line" lang="c"></span>
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7621
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7638
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<pre style="margin: 0;"> <span id="LC7638" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">alt_blocks</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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7622
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7639
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<pre style="margin: 0;"> <span id="LC7639" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">Genome_mark_mismatches_ref</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">genomic</span><span class="p">),</span><span class="n" style="color: #333;">querylength</span><span class="p">,</span><span class="n" style="color: #333;">query_compress</span><span class="p">,</span></span>
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<td class="diff-line-num old_line" data-linenumber="7623" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7623
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7640
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<pre style="margin: 0;"> <span id="LC7640" class="line" lang="c"> <span class="n" style="color: #333;">left</span><span class="p">,</span><span class="n" style="color: #333;">pos5</span><span class="p">,</span><span class="n" style="color: #333;">pos3</span><span class="p">,</span><span class="n" style="color: #333;">plusp</span><span class="p">,</span><span class="n" style="color: #333;">genestrand</span><span class="p">);</span></span>
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<a href="https://salsa.debian.org/med-team/gmap/-/compare/e36c478dd913ea44b8ccff832e1ed3c2409790ca...c42803c614bca47c818ce65af0a53b368a57e334#d747f527041a6e797f86fcd6f1fcd1562bab24a2"><strong>src/gmap.c</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">rcsid</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"$Id: gmap.c 2231<span class="idiff left right">16 2020-10-06 18:07:46</span>Z twu $"</span><span class="p">;</span></span>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">rcsid</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"$Id: gmap.c 2231<span class="idiff left right">99 2020-10-15 22:26:59</span>Z twu $"</span><span class="p">;</span></span>
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2
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifdef HAVE_CONFIG_H</span></span>
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3
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <config.h></span></span>
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4
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -461,6 +461,7 @@ static bool strictp = true;</td>
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461
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461
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<pre style="margin: 0;"> <span id="LC461" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/* static int proteinmode = 1; */</span></span>
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462
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462
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<pre style="margin: 0;"> <span id="LC462" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">uncompressedp</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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463
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463
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<pre style="margin: 0;"> <span id="LC463" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">nointronlenp</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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464
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<pre style="margin: 0;">+<span id="LC464" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">print_margin_p</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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464
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465
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<pre style="margin: 0;"> <span id="LC465" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">invertmode</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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465
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466
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<pre style="margin: 0;"> <span id="LC466" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ngap</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">3</span><span class="p">;</span></span>
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466
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467
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<pre style="margin: 0;"> <span id="LC467" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">wraplength</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">50</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="654" style="width: 35px; color: rgba(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="655" style="width: 35px; color: rgba(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">@@ -654,7 +655,8 @@ static struct option long_options[] = {</td>
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654
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655
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<pre style="margin: 0;"> <span id="LC655" class="line" lang="c"> <span class="p">{</span><span class="s" style="color: #d14;">"direction"</span><span class="p">,</span> <span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="sc" style="color: #d14;">'z'</span><span class="p">},</span> <span class="cm" style="color: #998; font-style: italic;">/* sense_try, sense_filter */</span></span>
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655
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656
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<pre style="margin: 0;"> <span id="LC656" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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656
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657
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<pre style="margin: 0;"> <span id="LC657" class="line" lang="c"> <span class="p">{</span><span class="s" style="color: #d14;">"tolerant"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="sc" style="color: #d14;">'Y'</span><span class="p">},</span> <span class="cm" style="color: #998; font-style: italic;">/* strictp */</span></span>
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657
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<pre style="margin: 0;">-<span id="LC657" class="line" lang="c"> <span class="p">{</span><span class="s" style="color: #d14;">"nolengths"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="sc" style="color: #d14;">'N'</span><span class="p">},</span> <span class="cm" style="color: #998; font-style: italic;">/* nointronlenp */</span></span>
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658
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<pre style="margin: 0;">+<span id="LC658" class="line" lang="c"> <span class="p">{</span><span class="s" style="color: #d14;">"nolengths"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">},</span> <span class="cm" style="color: #998; font-style: italic;">/* nointronlenp */</span></span>
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659
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<pre style="margin: 0;">+<span id="LC659" class="line" lang="c"> <span class="p">{</span><span class="s" style="color: #d14;">"nomargin"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">},</span> <span class="cm" style="color: #998; font-style: italic;">/* print_margin_p */</span></span>
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658
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660
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<pre style="margin: 0;"> <span id="LC660" class="line" lang="c"> <span class="p">{</span><span class="s" style="color: #d14;">"invertmode"</span><span class="p">,</span> <span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="sc" style="color: #d14;">'I'</span><span class="p">},</span> <span class="cm" style="color: #998; font-style: italic;">/* invertmode */</span></span>
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659
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661
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<pre style="margin: 0;"> <span id="LC661" class="line" lang="c"> <span class="p">{</span><span class="s" style="color: #d14;">"introngap"</span><span class="p">,</span> <span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="sc" style="color: #d14;">'i'</span><span class="p">},</span> <span class="cm" style="color: #998; font-style: italic;">/* ngap */</span></span>
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660
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662
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<pre style="margin: 0;"> <span id="LC662" class="line" lang="c"> <span class="p">{</span><span class="s" style="color: #d14;">"wraplength"</span><span class="p">,</span> <span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="sc" style="color: #d14;">'l'</span><span class="p">},</span> <span class="cm" style="color: #998; font-style: italic;">/* wraplength */</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="5701" style="width: 35px; color: rgba(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="5703" style="width: 35px; color: rgba(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">@@ -5701,9 +5703,9 @@ parse_command_line (int argc, char *argv[], int optind) {</td>
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5701
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5703
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<pre style="margin: 0;"> <span id="LC5703" class="line" lang="c"></span>
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5702
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5704
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<pre style="margin: 0;"> <span id="LC5704" class="line" lang="c"> <span class="k" style="font-weight: 600;">while</span> <span class="p">((</span><span class="n" style="color: #333;">opt</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">getopt_long</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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5703
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5705
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<pre style="margin: 0;"> <span id="LC5705" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifdef PMAP</span></span>
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5704
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<pre style="margin: 0;">-<span id="LC5704" class="line" lang="c"> <span class="s" style="color: #d14;">"q:D:a:d:k:g:2B:K:w:L:x:1t:s:c:SA03468:9n:f:ZO5o:V:v:M:m:ebu:E:PQY<span class="idiff left right">N</span>I:i:l:"</span><span class="p">,</span></span>
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5706
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<pre style="margin: 0;">+<span id="LC5706" class="line" lang="c"> <span class="s" style="color: #d14;">"q:D:a:d:k:g:2B:K:w:L:x:1t:s:c:SA03468:9n:f:ZO5o:V:v:M:m:ebu:E:PQYI:i:l:"</span><span class="p">,</span></span>
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5705
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5707
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<pre style="margin: 0;"> <span id="LC5707" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#else</span></span>
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5706
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<pre style="margin: 0;">-<span id="LC5706" class="line" lang="c"> <span class="s" style="color: #d14;">"q:D:d:k:g:2B:K:w:L:x:1t:s:c:p:SA03468:9n:f:ZO5o:V:v:M:m:ebu:E:PQFa:Tz:j:Y<span class="idiff left right">N</span>I:i:l:"</span><span class="p">,</span></span>
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5708
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<pre style="margin: 0;">+<span id="LC5708" class="line" lang="c"> <span class="s" style="color: #d14;">"q:D:d:k:g:2B:K:w:L:x:1t:s:c:p:SA03468:9n:f:ZO5o:V:v:M:m:ebu:E:PQFa:Tz:j:YI:i:l:"</span><span class="p">,</span></span>
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5707
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<td class="diff-line-num new_line" data-linenumber="5709" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5709
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<pre style="margin: 0;"> <span id="LC5709" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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5708
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<td class="diff-line-num new_line" data-linenumber="5710" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5710
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<pre style="margin: 0;"> <span id="LC5710" class="line" lang="c"> <span class="n" style="color: #333;">long_options</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">long_option_index</span><span class="p">))</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 class="p">{</span></span>
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5709
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<td class="diff-line-num new_line" data-linenumber="5711" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5711
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<pre style="margin: 0;"> <span id="LC5711" class="line" lang="c"> <span class="k" style="font-weight: 600;">switch</span> <span class="p">(</span><span class="n" style="color: #333;">opt</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="5878" style="width: 35px; color: rgba(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="5880" style="width: 35px; color: rgba(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">@@ -5878,6 +5880,10 @@ parse_command_line (int argc, char *argv[], int optind) {</td>
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5878
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<td class="diff-line-num new_line" data-linenumber="5880" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5880
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<pre style="margin: 0;"> <span id="LC5880" class="line" lang="c"> <span class="n" style="color: #333;">output_buffer_size</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">atoi</span><span class="p">(</span><span class="n" style="color: #333;">check_valid_int</span><span class="p">(</span><span class="n" style="color: #333;">optarg</span><span class="p">));</span></span>
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<td class="diff-line-num old_line" data-linenumber="5879" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5879
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<td class="diff-line-num new_line" data-linenumber="5881" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5881
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<pre style="margin: 0;"> <span id="LC5881" class="line" lang="c"> <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="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">strcmp</span><span class="p">(</span><span class="n" style="color: #333;">long_name</span><span class="p">,</span><span class="s" style="color: #d14;">"print-comment"</span><span class="p">))</span> <span class="p">{</span></span>
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5880
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<td class="diff-line-num new_line" data-linenumber="5882" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5882
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<pre style="margin: 0;"> <span id="LC5882" class="line" lang="c"> <span class="n" style="color: #333;">print_comment_p</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="5883" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
5883
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<pre style="margin: 0;">+<span id="LC5883" class="line" lang="c"> <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="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">strcmp</span><span class="p">(</span><span class="n" style="color: #333;">long_name</span><span class="p">,</span><span class="s" style="color: #d14;">"nolengths"</span><span class="p">))</span> <span class="p">{</span></span>
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<td class="diff-line-num new old_line" data-linenumber="5881" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="5884" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
5884
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<pre style="margin: 0;">+<span id="LC5884" class="line" lang="c"> <span class="n" style="color: #333;">nointronlenp</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="5885" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
5885
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<pre style="margin: 0;">+<span id="LC5885" class="line" lang="c"> <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="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">strcmp</span><span class="p">(</span><span class="n" style="color: #333;">long_name</span><span class="p">,</span><span class="s" style="color: #d14;">"nomargin"</span><span class="p">))</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="5886" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
5886
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<pre style="margin: 0;">+<span id="LC5886" class="line" lang="c"> <span class="n" style="color: #333;">print_margin_p</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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5881
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<td class="diff-line-num new_line" data-linenumber="5887" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5887
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<pre style="margin: 0;"> <span id="LC5887" class="line" lang="c"> <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="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">strcmp</span><span class="p">(</span><span class="n" style="color: #333;">long_name</span><span class="p">,</span><span class="s" style="color: #d14;">"failsonly"</span><span class="p">))</span> <span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="5882" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5882
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<td class="diff-line-num new_line" data-linenumber="5888" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5888
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<pre style="margin: 0;"> <span id="LC5888" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">nofailsp</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">)</span> <span class="p">{</span></span>
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5883
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<td class="diff-line-num new_line" data-linenumber="5889" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5889
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<pre style="margin: 0;"> <span id="LC5889" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span><span class="s" style="color: #d14;">"Cannot specify both --nofails and --failsonly</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="6330" style="width: 35px; color: rgba(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="6336" style="width: 35px; color: rgba(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">@@ -6330,7 +6336,6 @@ parse_command_line (int argc, char *argv[], int optind) {</td>
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6330
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6336
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<pre style="margin: 0;"> <span id="LC6336" class="line" lang="c"></span>
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6331
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6337
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<pre style="margin: 0;"> <span id="LC6337" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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<td class="diff-line-num old_line" data-linenumber="6332" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6332
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<td class="diff-line-num new_line" data-linenumber="6338" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6338
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<pre style="margin: 0;"> <span id="LC6338" class="line" lang="c"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'Y'</span><span class="p">:</span> <span class="n" style="color: #333;">strictp</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>
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6333
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<td class="diff-line-num new_line old" data-linenumber="6339" 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="LC6333" class="line" lang="c"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'N'</span><span class="p">:</span> <span class="n" style="color: #333;">nointronlenp</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="6334" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6334
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<td class="diff-line-num new_line" data-linenumber="6339" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6339
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<pre style="margin: 0;"> <span id="LC6339" class="line" lang="c"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'I'</span><span class="p">:</span> <span class="n" style="color: #333;">invertmode</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">atoi</span><span class="p">(</span><span class="n" style="color: #333;">check_valid_int</span><span class="p">(</span><span class="n" style="color: #333;">optarg</span><span class="p">));</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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6335
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6340
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<pre style="margin: 0;"> <span id="LC6340" class="line" lang="c"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'i'</span><span class="p">:</span> <span class="n" style="color: #333;">user_ngap</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">atoi</span><span class="p">(</span><span class="n" style="color: #333;">check_valid_int</span><span class="p">(</span><span class="n" style="color: #333;">optarg</span><span class="p">));</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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6336
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6341
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<pre style="margin: 0;"> <span id="LC6341" class="line" lang="c"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'l'</span><span class="p">:</span> <span class="n" style="color: #333;">wraplength</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">atoi</span><span class="p">(</span><span class="n" style="color: #333;">check_valid_int</span><span class="p">(</span><span class="n" style="color: #333;">optarg</span><span class="p">));</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="7035" style="width: 35px; color: rgba(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">@@ -7030,7 +7035,7 @@ main (int argc, char *argv[]) {</td>
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7030
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7035
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<pre style="margin: 0;"> <span id="LC7035" class="line" lang="c"> <span class="n" style="color: #333;">donor_typeint</span><span class="p">,</span><span class="n" style="color: #333;">acceptor_typeint</span><span class="p">);</span></span>
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7031
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<td class="diff-line-num new_line" data-linenumber="7036" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7036
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<pre style="margin: 0;"> <span id="LC7036" class="line" lang="c"> <span class="n" style="color: #333;">Dynprog_end_setup</span><span class="p">(</span><span class="n" style="color: #333;">splicesites</span><span class="p">,</span><span class="n" style="color: #333;">splicetypes</span><span class="p">,</span><span class="n" style="color: #333;">splicedists</span><span class="p">,</span><span class="n" style="color: #333;">nsplicesites</span><span class="p">,</span></span>
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7032
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<td class="diff-line-num new_line" data-linenumber="7037" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7037
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<pre style="margin: 0;"> <span id="LC7037" class="line" lang="c"> <span class="n" style="color: #333;">trieoffsets_obs</span><span class="p">,</span><span class="n" style="color: #333;">triecontents_obs</span><span class="p">,</span><span class="n" style="color: #333;">trieoffsets_max</span><span class="p">,</span><span class="n" style="color: #333;">triecontents_max</span><span class="p">);</span></span>
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7033
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<pre style="margin: 0;">-<span id="LC7033" class="line" lang="c"> <span class="n" style="color: #333;">Pair_setup</span><span class="p">(</span><span class="n" style="color: #333;">novelsplicingp</span><span class="p">,</span><span class="n" style="color: #333;">splicing_iit</span><span class="p">,</span><span class="n" style="color: #333;">trim_indel_score</span><span class="p">,</span></span>
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7038
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<pre style="margin: 0;">+<span id="LC7038" class="line" lang="c"> <span class="n" style="color: #333;">Pair_setup</span><span class="p">(</span><span class="n" style="color: #333;">novelsplicingp</span><span class="p">,</span><span class="n" style="color: #333;">splicing_iit</span><span class="p">,</span><span class="n" style="color: #333;">trim_indel_score</span><span class="p">,</span><span class="n" style="color: #333;"><span class="idiff left">print_margin_p</span></span><span class="p"><span class="idiff right">,</span></span></span>
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7034
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<td class="diff-line-num new_line" data-linenumber="7039" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7039
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<pre style="margin: 0;"> <span id="LC7039" class="line" lang="c"> <span class="n" style="color: #333;">gff3_separators_p</span><span class="p">,</span><span class="n" style="color: #333;">sam_insert_0M_p</span><span class="p">,</span><span class="n" style="color: #333;">force_xs_direction_p</span><span class="p">,</span></span>
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7035
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7040
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<pre style="margin: 0;"> <span id="LC7040" class="line" lang="c"> <span class="n" style="color: #333;">md_lowercase_variant_p</span><span class="p">,</span><span class="cm" style="color: #998; font-style: italic;">/*snps_p*/</span><span class="n" style="color: #333;">genomecomp_alt</span> <span class="o" style="font-weight: 600;">?</span> <span class="nb" style="color: #0086b3;">true</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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7036
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7041
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<pre style="margin: 0;"> <span id="LC7041" class="line" lang="c"> <span class="n" style="color: #333;">gff3_phase_swap_p</span><span class="p">,</span><span class="n" style="color: #333;">cdstype</span><span class="p">,</span><span class="n" style="color: #333;">sam_cigar_extended_p</span><span class="p">,</span><span class="n" style="color: #333;">cigar_action</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="7744" style="width: 35px; color: rgba(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">@@ -7739,7 +7744,8 @@ External map file options\n\</td>
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7739
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7744
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<pre style="margin: 0;"> <span id="LC7744" class="line" lang="c"></span>
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7740
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7745
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<pre style="margin: 0;"> <span id="LC7745" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stdout</span><span class="p">,</span><span class="s" style="color: #d14;">"\</span></span>
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7741
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7746
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<pre style="margin: 0;"> <span id="LC7746" class="line" lang="c"><span class="s" style="color: #d14;">Alignment output options</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">\</span></span>
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7742
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<pre style="margin: 0;">-<span id="LC7742" class="line" lang="c"><span class="s" style="color: #d14;"> -N, --nolengths No intron lengths in alignment</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">\</span></span>
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7747
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<pre style="margin: 0;">+<span id="LC7747" class="line" lang="c"><span class="s" style="color: #d14;"> --nolengths No intron lengths in alignment</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">\</span></span>
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<td class="diff-line-num new new_line" data-linenumber="7748" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
7748
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<pre style="margin: 0;">+<span id="LC7748" class="line" lang="c"><span class="s" style="color: #d14;"> --nomargin No left margin in GMAP standard output (with the -A flag)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">\</span></span>
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7743
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7749
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<pre style="margin: 0;"> <span id="LC7749" class="line" lang="c"><span class="s" style="color: #d14;"> -I, --invertmode=INT Mode for alignments to genomic (-) strand:</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">\</span></span>
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7744
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7750
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<pre style="margin: 0;"> <span id="LC7750" class="line" lang="c"><span class="s" style="color: #d14;"> 0=Don't invert the cDNA (default)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">\</span></span>
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7745
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7751
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<pre style="margin: 0;"> <span id="LC7751" class="line" lang="c"><span class="s" style="color: #d14;"> 1=Invert cDNA and print genomic (-) strand</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">\</span></span>
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<a href="https://salsa.debian.org/med-team/gmap/-/compare/e36c478dd913ea44b8ccff832e1ed3c2409790ca...c42803c614bca47c818ce65af0a53b368a57e334#c98399a907bb515fa302e9111b148f9f0da3c8ba"><strong>src/kmer-search.c</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">rcsid</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"$Id: kmer-search.c 22<span class="idiff left right">2813 2020-06-03 22:02:45</span>Z twu $"</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">rcsid</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"$Id: kmer-search.c 22<span class="idiff left right">3197 2020-10-15 22:23:47</span>Z twu $"</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifdef HAVE_CONFIG_H</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <config.h></span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1368,17 +1368,21 @@ single_hits_gminus (int *found_score_overall, int *found_score_within_trims,</td>
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<pre style="margin: 0;"> <span id="LC1368" class="line" lang="c"> <span class="n" style="color: #333;">pos3</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">univdiagonal</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">queryend</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">genomelength</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">querylength</span><span class="p">)</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">queryend</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="p">(</span><span class="n" style="color: #333;">genomelength</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">left</span><span class="p">);</span></span>
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1369
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1369
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<pre style="margin: 0;"> <span id="LC1369" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC1370" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"tr gminus query %d..%d, align %u..%u [%u..%u], left %u = %u - (%d - %d)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span></span>
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1371
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<pre style="margin: 0;">-<span id="LC1371" class="line" lang="c"> <span class="n" style="color: #333;">query<span class="idiff left">length</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">queryend</span></span><span class="p"><span class="idiff">,</span></span><span class="n" style="color: #333;"><span class="idiff">querylength</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">querystart</span></span><span class="p">,</span><span class="n" style="color: #333;">alignstart</span><span class="p">,</span><span class="n" style="color: #333;">alignend</span><span class="p">,</span><span class="n" style="color: #333;">alignstart</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">chroffset</span><span class="p">,</span><span class="n" style="color: #333;">alignend</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">chroffset</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC1371" class="line" lang="c"> <span class="n" style="color: #333;">query<span class="idiff left">start</span></span><span class="p"><span class="idiff">,</span></span><span class="n" style="color: #333;"><span class="idiff right">queryend</span></span><span class="p">,</span><span class="n" style="color: #333;">alignstart</span><span class="p">,</span><span class="n" style="color: #333;">alignend</span><span class="p">,</span><span class="n" style="color: #333;">alignstart</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">chroffset</span><span class="p">,</span><span class="n" style="color: #333;">alignend</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">chroffset</span><span class="p">,</span></span>
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1372
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<pre style="margin: 0;"> <span id="LC1372" class="line" lang="c"> <span class="n" style="color: #333;">left</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">chroffset</span><span class="p">,</span><span class="n" style="color: #333;">alignend</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">chroffset</span><span class="p">,</span><span class="n" style="color: #333;">querylength</span><span class="p">,</span><span class="n" style="color: #333;">queryend</span><span class="p">));</span></span>
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<pre style="margin: 0;">+<span id="LC1373" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC1374" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Verified that (querylength - pos3) and (querylength - pos5)</span></span>
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1375
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<pre style="margin: 0;">+<span id="LC1375" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> are correct here, possibly because of how querystart and</span></span>
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<pre style="margin: 0;">+<span id="LC1376" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> queryend are defined above*/</span></span>
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1377
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<pre style="margin: 0;"> <span id="LC1377" class="line" lang="c"> <span class="n" style="color: #333;">nmismatches</span> <span class="o" style="font-weight: 600;">=</span></span>
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1374
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1378
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<pre style="margin: 0;"> <span id="LC1378" class="line" lang="c"> <span class="n" style="color: #333;">Genome_count_mismatches_substring</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">ref_nmismatches</span><span class="p">,</span><span class="n" style="color: #333;">genomebits</span><span class="p">,</span><span class="n" style="color: #333;">genomebits_alt</span><span class="p">,</span><span class="n" style="color: #333;">query_compress_rev</span><span class="p">,</span><span class="n" style="color: #333;">left</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC1375" class="line" lang="c"> <span class="n" style="color: #333;"><span class="idiff left">pos5</span></span><span class="p"><span class="idiff">,</span></span><span class="n" style="color: #333;"><span class="idiff right">pos3</span></span><span class="p">,</span><span class="cm" style="color: #998; font-style: italic;">/*plusp*/</span><span class="nb" style="color: #0086b3;">false</span><span class="p">,</span><span class="cm" style="color: #998; font-style: italic;">/*genestrand*/</span><span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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1379
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<pre style="margin: 0;">+<span id="LC1379" class="line" lang="c"> <span class="n" style="color: #333;"><span class="idiff left">querylength</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pos3</span></span><span class="p"><span class="idiff">,</span></span><span class="n" style="color: #333;"><span class="idiff">querylength</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">pos5</span></span><span class="p">,</span><span class="cm" style="color: #998; font-style: italic;">/*plusp*/</span><span class="nb" style="color: #0086b3;">false</span><span class="p">,</span><span class="cm" style="color: #998; font-style: italic;">/*genestrand*/</span><span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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1376
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1380
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<pre style="margin: 0;"> <span id="LC1380" class="line" lang="c"> <span class="n" style="color: #333;">nmismatches_whole</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">nmismatches</span><span class="p">;</span></span>
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1377
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1381
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<pre style="margin: 0;"> <span id="LC1381" class="line" lang="c"> <span class="n" style="color: #333;">nmismatches_refdiff</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">ref_nmismatches</span><span class="p">;</span></span>
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1378
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<td class="diff-line-num new_line" data-linenumber="1382" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1382
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<pre style="margin: 0;"> <span id="LC1382" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"mismatches rev from %d to %d: %d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">pos5</span><span class="p">,</span><span class="n" style="color: #333;">pos3</span><span class="p">,</span><span class="n" style="color: #333;">nmismatches</span><span class="p">));</span></span>
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1379
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1383
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<pre style="margin: 0;"> <span id="LC1383" class="line" lang="c"></span>
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1380
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<td class="diff-line-num new_line old" data-linenumber="1384" 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="LC1380" class="line" lang="c"> <span class="k" style="font-weight: 600;"><span class="idiff left">if</span></span><span class="idiff"> </span><span class="p"><span class="idiff">((</span></span><span class="n" style="color: #333;"><span class="idiff">substring</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">Substring_new</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">nmismatches</span></span><span class="p"><span class="idiff">,</span></span><span class="n" style="color: #333;"><span class="idiff">ref_nmismatches</span></span><span class="p"><span class="idiff">,</span></span><span class="n" style="color: #333;"><span class="idiff">left</span></span><span class="p"><span class="idiff right">,</span></span></span>
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1381
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<pre style="margin: 0;">-<span id="LC1381" class="line" lang="c"><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">querylength</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pos3</span></span><span class="p"><span class="idiff">,</span></span><span class="n" style="color: #333;"><span class="idiff">querylength</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">pos5</span></span><span class="p">,</span><span class="n" style="color: #333;">querylength</span><span class="p">,</span></span>
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1384
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<pre style="margin: 0;">+<span id="LC1384" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;"><span class="idiff left right">/* Verified that pos5 and pos3 are correct */</span></span></span>
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1385
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<pre style="margin: 0;">+<span id="LC1385" class="line" lang="c"><span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">if</span></span><span class="idiff"> </span><span class="p"><span class="idiff">((</span></span><span class="n" style="color: #333;"><span class="idiff">substring</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">Substring_new</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">nmismatches</span></span><span class="p"><span class="idiff">,</span></span><span class="n" style="color: #333;"><span class="idiff">ref_nmismatches</span></span><span class="p"><span class="idiff">,</span></span><span class="n" style="color: #333;"><span class="idiff">left</span></span><span class="p"><span class="idiff">,</span></span><span class="n" style="color: #333;"><span class="idiff">pos5</span></span><span class="p"><span class="idiff">,</span></span><span class="n" style="color: #333;"><span class="idiff right">pos3</span></span><span class="p">,</span><span class="n" style="color: #333;">querylength</span><span class="p">,</span></span>
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1382
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1386
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<pre style="margin: 0;"> <span id="LC1386" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/*plusp*/</span><span class="nb" style="color: #0086b3;">false</span><span class="p">,</span><span class="cm" style="color: #998; font-style: italic;">/*genestrand*/</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="n" style="color: #333;">query_compress_rev</span><span class="p">,</span></span>
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1383
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<td class="diff-line-num new_line" data-linenumber="1387" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1387
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<pre style="margin: 0;"> <span id="LC1387" class="line" lang="c"> <span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">chrnum</span><span class="p">,</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">chroffset</span><span class="p">,</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">chrhigh</span><span class="p">,</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">chrlength</span><span class="p">,</span></span>
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1384
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<td class="diff-line-num new_line" data-linenumber="1388" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1388
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<pre style="margin: 0;"> <span id="LC1388" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/*splice_querystart_p*/</span><span class="nb" style="color: #0086b3;">false</span><span class="p">,</span><span class="cm" style="color: #998; font-style: italic;">/*splicetype_querystart*/</span><span class="n" style="color: #333;">NO_SPLICE</span><span class="p">,</span><span class="cm" style="color: #998; font-style: italic;">/*ambig_prob_querystart*/</span><span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mi" style="color: #099;">0</span><span class="p">,</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1735" style="width: 35px; color: rgba(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="1739" style="width: 35px; color: rgba(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">@@ -1735,7 +1739,7 @@ search_transcriptome_complete (Path_T **tplus_gplus_paths, int *n_tplus_gplus,</td>
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1735
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1739
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<pre style="margin: 0;"> <span id="LC1739" class="line" lang="c"> <span class="n" style="color: #333;">total_nmismatches</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Genome_count_mismatches_substring</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">ref_nmismatches</span><span class="p">,</span><span class="n" style="color: #333;">transcriptomebits</span><span class="p">,</span><span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span><span class="n" style="color: #333;">query_compress_fwd</span><span class="p">,</span></span>
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<td class="diff-line-num old_line" data-linenumber="1736" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1736
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<td class="diff-line-num new_line" data-linenumber="1740" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1740
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<pre style="margin: 0;"> <span id="LC1740" class="line" lang="c"> <span class="n" style="color: #333;">tr_left</span><span class="p">,</span><span class="cm" style="color: #998; font-style: italic;">/*pos5*/</span><span class="n" style="color: #333;">trim5</span><span class="p">,</span><span class="cm" style="color: #998; font-style: italic;">/*pos3*/</span><span class="n" style="color: #333;">queryend</span><span class="p">,</span><span class="cm" style="color: #998; font-style: italic;">/*plusp*/</span><span class="nb" style="color: #0086b3;">true</span><span class="p">,</span><span class="cm" style="color: #998; font-style: italic;">/*genestrand*/</span><span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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1737
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1741
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<pre style="margin: 0;"> <span id="LC1741" class="line" lang="c"></span>
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1738
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<pre style="margin: 0;">-<span id="LC1738" class="line" lang="c"> <span class="n" style="color: #333;">total_nmatches</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left right">querylength</span></span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">total_nmismatches</span><span class="p">;</span></span>
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1742
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<pre style="margin: 0;">+<span id="LC1742" class="line" lang="c"> <span class="n" style="color: #333;">total_nmatches</span> <span class="o" style="font-weight: 600;">=</span> <span class="p"><span class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">querylength</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">trim5</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">trim3</span></span><span class="p"><span class="idiff right">)</span></span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">total_nmismatches</span><span class="p">;</span></span>
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1743
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<pre style="margin: 0;"> <span id="LC1743" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"tplus diagonal %u => trimmed %d..%d, nmismatches: %d total, %d at 5', and %d at 3'. total_nmatches: %d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span></span>
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1744
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<pre style="margin: 0;"> <span id="LC1744" class="line" lang="c"> <span class="n" style="color: #333;">tr_univdiagonal</span><span class="p">,</span><span class="n" style="color: #333;">trim5</span><span class="p">,</span><span class="n" style="color: #333;">querylength</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">trim3</span><span class="p">,</span><span class="n" style="color: #333;">total_nmismatches</span><span class="p">,</span><span class="n" style="color: #333;">nmismatches5</span><span class="p">,</span><span class="n" style="color: #333;">nmismatches3</span><span class="p">,</span></span>
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1745
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<pre style="margin: 0;"> <span id="LC1745" class="line" lang="c"> <span class="n" style="color: #333;">total_nmatches</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">@@ -1935,14 +1939,13 @@ search_transcriptome_complete (Path_T **tplus_gplus_paths, int *n_tplus_gplus,</td>
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1935
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1939
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<pre style="margin: 0;"> <span id="LC1939" class="line" lang="c"></span>
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1936
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1940
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<pre style="margin: 0;"> <span id="LC1940" class="line" lang="c"> <span class="n" style="color: #333;">endpoints</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">Uintlist_T</span><span class="p">)</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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1937
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1941
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<pre style="margin: 0;"> <span id="LC1941" class="line" lang="c"> <span class="n" style="color: #333;">gaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">Intlist_T</span><span class="p">)</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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1942
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<pre style="margin: 0;">+<span id="LC1942" class="line" lang="c"> <span class="n" style="color: #333;">abortp</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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1938
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1943
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<pre style="margin: 0;"> <span id="LC1943" class="line" lang="c"></span>
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1939
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1944
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<pre style="margin: 0;"> <span id="LC1944" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">q</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tr_lefts</span><span class="p">,</span> <span class="n" style="color: #333;">r</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">querystarts</span><span class="p">,</span> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">queryends</span><span class="p">,</span> <span class="n" style="color: #333;">t</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">adjustments</span><span class="p">;</span> <span class="n" style="color: #333;">q</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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1940
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1945
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<pre style="margin: 0;"> <span id="LC1945" class="line" lang="c"> <span class="n" style="color: #333;">q</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Uintlist_next</span><span class="p">(</span><span class="n" style="color: #333;">q</span><span class="p">),</span> <span class="n" style="color: #333;">r</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Intlist_next</span><span class="p">(</span><span class="n" style="color: #333;">r</span><span class="p">),</span> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Intlist_next</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">))</span> <span class="p">{</span></span>
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1941
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1946
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<pre style="margin: 0;"> <span id="LC1946" class="line" lang="c"> <span class="n" style="color: #333;">transcript_diag</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Uintlist_head</span><span class="p">(</span><span class="n" style="color: #333;">q</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">troffset</span><span class="p">;</span></span>
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1942
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1947
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<pre style="margin: 0;"> <span id="LC1947" class="line" lang="c"></span>
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1943
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1948
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<pre style="margin: 0;"> <span id="LC1948" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Find initial exonpos */</span></span>
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<pre style="margin: 0;">-<span id="LC1944" class="line" lang="c"> <span class="n" style="color: #333;">abortp</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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1945
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<pre style="margin: 0;">-<span id="LC1945" class="line" lang="c"></span>
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1946
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1949
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<pre style="margin: 0;"> <span id="LC1949" class="line" lang="c"> <span class="n" style="color: #333;">querystart</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Intlist_head</span><span class="p">(</span><span class="n" style="color: #333;">r</span><span class="p">);</span> <span class="cm" style="color: #998; font-style: italic;">/* tplus: compute from querystart to queryend */</span></span>
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1947
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1950
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<pre style="margin: 0;"> <span id="LC1950" class="line" lang="c"> <span class="n" style="color: #333;">queryend</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Intlist_head</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">);</span></span>
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1948
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1951
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<pre style="margin: 0;"> <span id="LC1951" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</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;">Analyzing query %d..%d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">querystart</span><span class="p">,</span><span class="n" style="color: #333;">queryend</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">@@ -2057,7 +2060,7 @@ search_transcriptome_complete (Path_T **tplus_gplus_paths, int *n_tplus_gplus,</td>
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2057
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2060
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<pre style="margin: 0;"> <span id="LC2060" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">abortp</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="2058" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2058
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<td class="diff-line-num new_line" data-linenumber="2061" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2061
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<pre style="margin: 0;"> <span id="LC2061" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Skip */</span></span>
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2059
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<td class="diff-line-num new_line" data-linenumber="2062" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2062
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<pre style="margin: 0;"> <span id="LC2062" class="line" lang="c"> <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="cm" style="color: #998; font-style: italic;">/* len <= nindels ||*/</span><span class="n" style="color: #333;">exon_residual</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">nindels</span><span class="p">)</span> <span class="p">{</span></span>
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2060
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<td class="diff-line-num new_line old" data-linenumber="2063" 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="LC2060" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"ABORTING BECAUSE INDEL OVERLAPS SPLICE SITE</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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2063
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<pre style="margin: 0;">+<span id="LC2063" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"ABORTING BECAUSE INDEL OVERLAPS SPLICE SITE<span class="idiff left right"> (1)</span></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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2061
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2064
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<pre style="margin: 0;"> <span id="LC2064" class="line" lang="c"> <span class="n" style="color: #333;">abortp</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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2062
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2065
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<pre style="margin: 0;"> <span id="LC2065" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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2063
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2066
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<pre style="margin: 0;"> <span id="LC2066" class="line" lang="c"> <span class="n" style="color: #333;">gaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Intlist_push</span><span class="p">(</span><span class="n" style="color: #333;">gaps</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;">adj</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2091" style="width: 35px; color: rgba(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="2094" style="width: 35px; color: rgba(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">@@ -2091,14 +2094,13 @@ search_transcriptome_complete (Path_T **tplus_gplus_paths, int *n_tplus_gplus,</td>
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2091
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2094
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<pre style="margin: 0;"> <span id="LC2094" class="line" lang="c"> </span>
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2092
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2095
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<pre style="margin: 0;"> <span id="LC2095" class="line" lang="c"> <span class="n" style="color: #333;">endpoints</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">Uintlist_T</span><span class="p">)</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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2093
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2096
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<pre style="margin: 0;"> <span id="LC2096" class="line" lang="c"> <span class="n" style="color: #333;">gaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">Intlist_T</span><span class="p">)</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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2097
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<pre style="margin: 0;">+<span id="LC2097" class="line" lang="c"> <span class="n" style="color: #333;">abortp</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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2094
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2098
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<pre style="margin: 0;"> <span id="LC2098" class="line" lang="c"> </span>
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2095
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2099
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<pre style="margin: 0;"> <span id="LC2099" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">q</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tr_lefts</span><span class="p">,</span> <span class="n" style="color: #333;">r</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">querystarts</span><span class="p">,</span> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">queryends</span><span class="p">,</span> <span class="n" style="color: #333;">t</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">adjustments</span><span class="p">;</span> <span class="n" style="color: #333;">q</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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2096
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<td class="diff-line-num new_line" data-linenumber="2100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2100
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<pre style="margin: 0;"> <span id="LC2100" class="line" lang="c"> <span class="n" style="color: #333;">q</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Uintlist_next</span><span class="p">(</span><span class="n" style="color: #333;">q</span><span class="p">),</span> <span class="n" style="color: #333;">r</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Intlist_next</span><span class="p">(</span><span class="n" style="color: #333;">r</span><span class="p">),</span> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Intlist_next</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">))</span> <span class="p">{</span></span>
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2097
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2101
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<pre style="margin: 0;"> <span id="LC2101" class="line" lang="c"> <span class="n" style="color: #333;">transcript_diag</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Uintlist_head</span><span class="p">(</span><span class="n" style="color: #333;">q</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">troffset</span><span class="p">;</span></span>
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2098
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2102
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<pre style="margin: 0;"> <span id="LC2102" class="line" lang="c"></span>
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2099
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2103
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<pre style="margin: 0;"> <span id="LC2103" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Find initial exonpos */</span></span>
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2100
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<pre style="margin: 0;">-<span id="LC2100" class="line" lang="c"> <span class="n" style="color: #333;">abortp</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="2101" 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">
2101
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<td class="diff-line-num new_line old" data-linenumber="2104" 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="LC2101" class="line" lang="c"></span>
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2102
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2104
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<pre style="margin: 0;"> <span id="LC2104" class="line" lang="c"> <span class="n" style="color: #333;">querystart</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Intlist_head</span><span class="p">(</span><span class="n" style="color: #333;">r</span><span class="p">);</span> <span class="cm" style="color: #998; font-style: italic;">/* tplus: compute from querystart to queryend */</span></span>
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2103
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2105
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<pre style="margin: 0;"> <span id="LC2105" class="line" lang="c"> <span class="n" style="color: #333;">queryend</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Intlist_head</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">);</span></span>
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2104
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2106
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<pre style="margin: 0;"> <span id="LC2106" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</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;">Analyzing query %d..%d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">querystart</span><span class="p">,</span><span class="n" style="color: #333;">queryend</span><span class="p">));</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2212" style="width: 35px; color: rgba(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="2214" style="width: 35px; color: rgba(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">@@ -2212,7 +2214,7 @@ search_transcriptome_complete (Path_T **tplus_gplus_paths, int *n_tplus_gplus,</td>
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2212
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2214
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<pre style="margin: 0;"> <span id="LC2214" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">abortp</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">)</span> <span class="p">{</span></span>
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2213
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<td class="diff-line-num new_line" data-linenumber="2215" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2215
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<pre style="margin: 0;"> <span id="LC2215" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Skip */</span></span>
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2214
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2216
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<pre style="margin: 0;"> <span id="LC2216" class="line" lang="c"> <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="cm" style="color: #998; font-style: italic;">/*len <= nindels ||*/</span> <span class="n" style="color: #333;">exon_residual</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">nindels</span><span class="p">)</span> <span class="p">{</span></span>
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2215
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<pre style="margin: 0;">-<span id="LC2215" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"ABORTING BECAUSE INDEL OVERLAPS SPLICE SITE</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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2217
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<pre style="margin: 0;">+<span id="LC2217" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"ABORTING BECAUSE INDEL OVERLAPS SPLICE SITE<span class="idiff left right"> (2)</span></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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2216
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2218
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<pre style="margin: 0;"> <span id="LC2218" class="line" lang="c"> <span class="n" style="color: #333;">abortp</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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2217
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2219
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<pre style="margin: 0;"> <span id="LC2219" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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2218
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2220
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<pre style="margin: 0;"> <span id="LC2220" class="line" lang="c"> <span class="n" style="color: #333;">gaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Intlist_push</span><span class="p">(</span><span class="n" style="color: #333;">gaps</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;">adj</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2283" style="width: 35px; color: rgba(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="2285" style="width: 35px; color: rgba(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">@@ -2283,10 +2285,11 @@ search_transcriptome_complete (Path_T **tplus_gplus_paths, int *n_tplus_gplus,</td>
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2283
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2285
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<pre style="margin: 0;"> <span id="LC2285" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/*plusp*/</span><span class="nb" style="color: #0086b3;">false</span><span class="p">,</span><span class="cm" style="color: #998; font-style: italic;">/*genestrand*/</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="cm" style="color: #998; font-style: italic;">/*query_unk_mismatch_local_p*/</span><span class="nb" style="color: #0086b3;">false</span><span class="p">,</span><span class="cm" style="color: #998; font-style: italic;">/*kmer*/</span><span class="n" style="color: #333;">index1part_tr</span><span class="p">);</span></span>
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2284
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2286
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<pre style="margin: 0;"> <span id="LC2286" class="line" lang="c"></span>
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2285
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2287
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<pre style="margin: 0;"> <span id="LC2287" class="line" lang="c"> <span class="n" style="color: #333;">trim3</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">querylength</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">queryend</span><span class="p">;</span></span>
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2288
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<pre style="margin: 0;">+<span id="LC2288" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Verified parameters to Genome_count_mismatches_substring */</span></span>
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2286
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2289
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<pre style="margin: 0;"> <span id="LC2289" class="line" lang="c"> <span class="n" style="color: #333;">total_nmismatches</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Genome_count_mismatches_substring</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">ref_nmismatches</span><span class="p">,</span><span class="n" style="color: #333;">transcriptomebits</span><span class="p">,</span><span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span><span class="n" style="color: #333;">query_compress_rev</span><span class="p">,</span></span>
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2287
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2290
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<pre style="margin: 0;"> <span id="LC2290" class="line" lang="c"> <span class="n" style="color: #333;">tr_left</span><span class="p">,</span><span class="cm" style="color: #998; font-style: italic;">/*pos5*/</span><span class="n" style="color: #333;">trim5</span><span class="p">,</span><span class="cm" style="color: #998; font-style: italic;">/*pos3*/</span><span class="n" style="color: #333;">queryend</span><span class="p">,</span><span class="cm" style="color: #998; font-style: italic;">/*plusp*/</span><span class="nb" style="color: #0086b3;">false</span><span class="p">,</span><span class="cm" style="color: #998; font-style: italic;">/*genestrand*/</span><span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC2291" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC2289" class="line" lang="c"> <span class="n" style="color: #333;">total_nmatches</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left right">querylength</span></span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">total_nmismatches</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC2292" class="line" lang="c"> <span class="n" style="color: #333;">total_nmatches</span> <span class="o" style="font-weight: 600;">=</span> <span class="p"><span class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">querylength</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">trim3</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">trim5</span></span><span class="p"><span class="idiff right">)</span></span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">total_nmismatches</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC2293" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"tminus diagonal %u => trimmed %d..%d, nmismatches: %d total, %d at 5', and %d at 3', total_nmatches: %d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC2294" class="line" lang="c"> <span class="n" style="color: #333;">tr_univdiagonal</span><span class="p">,</span><span class="n" style="color: #333;">trim5</span><span class="p">,</span><span class="n" style="color: #333;">querylength</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">trim3</span><span class="p">,</span><span class="n" style="color: #333;">total_nmismatches</span><span class="p">,</span><span class="n" style="color: #333;">nmismatches5</span><span class="p">,</span><span class="n" style="color: #333;">nmismatches3</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC2295" class="line" lang="c"> <span class="n" style="color: #333;">total_nmatches</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">@@ -2490,13 +2493,13 @@ search_transcriptome_complete (Path_T **tplus_gplus_paths, int *n_tplus_gplus,</td>
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<pre style="margin: 0;"> <span id="LC2493" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC2494" class="line" lang="c"> <span class="n" style="color: #333;">endpoints</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">Uintlist_T</span><span class="p">)</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC2495" class="line" lang="c"> <span class="n" style="color: #333;">gaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">Intlist_T</span><span class="p">)</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC2496" class="line" lang="c"> <span class="n" style="color: #333;">abortp</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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2497
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<pre style="margin: 0;"> <span id="LC2497" class="line" lang="c"></span>
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2498
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<pre style="margin: 0;"> <span id="LC2498" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">q</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tr_lefts</span><span class="p">,</span> <span class="n" style="color: #333;">r</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">querystarts</span><span class="p">,</span> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">queryends</span><span class="p">,</span> <span class="n" style="color: #333;">t</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">adjustments</span><span class="p">;</span> <span class="n" style="color: #333;">q</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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2499
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<pre style="margin: 0;"> <span id="LC2499" class="line" lang="c"> <span class="n" style="color: #333;">q</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Uintlist_next</span><span class="p">(</span><span class="n" style="color: #333;">q</span><span class="p">),</span> <span class="n" style="color: #333;">r</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Intlist_next</span><span class="p">(</span><span class="n" style="color: #333;">r</span><span class="p">),</span> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Intlist_next</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">))</span> <span class="p">{</span></span>
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2500
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<pre style="margin: 0;"> <span id="LC2500" class="line" lang="c"> <span class="n" style="color: #333;">transcript_diag</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Uintlist_head</span><span class="p">(</span><span class="n" style="color: #333;">q</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">troffset</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC2501" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC2502" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Find initial exonpos */</span></span>
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<pre style="margin: 0;">-<span id="LC2499" class="line" lang="c"> <span class="n" style="color: #333;">abortp</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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2503
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<pre style="margin: 0;"> <span id="LC2503" class="line" lang="c"> <span class="n" style="color: #333;">queryend</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Intlist_head</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">);</span> <span class="cm" style="color: #998; font-style: italic;">/* tminus: compute from queryend to querystart */</span></span>
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2501
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<td class="diff-line-num new_line" data-linenumber="2504" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2504
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<pre style="margin: 0;"> <span id="LC2504" class="line" lang="c"> <span class="n" style="color: #333;">querystart</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Intlist_head</span><span class="p">(</span><span class="n" style="color: #333;">r</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="2502" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2502
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2505
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<pre style="margin: 0;"> <span id="LC2505" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</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;">Analyzing query %d..%d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">querystart</span><span class="p">,</span><span class="n" style="color: #333;">queryend</span><span class="p">));</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2610" style="width: 35px; color: rgba(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="2613" style="width: 35px; color: rgba(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">@@ -2610,7 +2613,7 @@ search_transcriptome_complete (Path_T **tplus_gplus_paths, int *n_tplus_gplus,</td>
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2610
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<td class="diff-line-num new_line" data-linenumber="2613" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2613
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<pre style="margin: 0;"> <span id="LC2613" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">abortp</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="2611" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2611
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<td class="diff-line-num new_line" data-linenumber="2614" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2614
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<pre style="margin: 0;"> <span id="LC2614" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Skip */</span></span>
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<td class="diff-line-num old_line" data-linenumber="2612" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2612
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<td class="diff-line-num new_line" data-linenumber="2615" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2615
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<pre style="margin: 0;"> <span id="LC2615" class="line" lang="c"> <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="cm" style="color: #998; font-style: italic;">/*len <= nindels ||*/</span><span class="n" style="color: #333;">exon_residual</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">nindels</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="2613" 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">
2613
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<td class="diff-line-num new_line old" data-linenumber="2616" 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="LC2613" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"ABORTING BECAUSE INDEL OVERLAPS SPLICE SITE</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">));</span></span>
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<td class="diff-line-num new old_line" data-linenumber="2614" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="2616" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2616
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<pre style="margin: 0;">+<span id="LC2616" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"ABORTING BECAUSE INDEL OVERLAPS SPLICE SITE<span class="idiff left right"> (3)</span></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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2614
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<td class="diff-line-num new_line" data-linenumber="2617" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2617
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<pre style="margin: 0;"> <span id="LC2617" class="line" lang="c"> <span class="n" style="color: #333;">abortp</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="2615" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2615
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<td class="diff-line-num new_line" data-linenumber="2618" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2618
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<pre style="margin: 0;"> <span id="LC2618" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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2616
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<td class="diff-line-num new_line" data-linenumber="2619" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2619
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<pre style="margin: 0;"> <span id="LC2619" class="line" lang="c"> <span class="n" style="color: #333;">gaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Intlist_push</span><span class="p">(</span><span class="n" style="color: #333;">gaps</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;">adj</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2644" style="width: 35px; color: rgba(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="2647" style="width: 35px; color: rgba(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">@@ -2644,13 +2647,13 @@ search_transcriptome_complete (Path_T **tplus_gplus_paths, int *n_tplus_gplus,</td>
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2644
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2647
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<pre style="margin: 0;"> <span id="LC2647" class="line" lang="c"></span>
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2645
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<td class="diff-line-num new_line" data-linenumber="2648" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2648
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<pre style="margin: 0;"> <span id="LC2648" class="line" lang="c"> <span class="n" style="color: #333;">endpoints</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">Uintlist_T</span><span class="p">)</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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2646
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2649
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<pre style="margin: 0;"> <span id="LC2649" class="line" lang="c"> <span class="n" style="color: #333;">gaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">Intlist_T</span><span class="p">)</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2650" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2650
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<pre style="margin: 0;">+<span id="LC2650" class="line" lang="c"> <span class="n" style="color: #333;">abortp</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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2647
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<td class="diff-line-num new_line" data-linenumber="2651" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2651
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<pre style="margin: 0;"> <span id="LC2651" class="line" lang="c"></span>
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<td class="diff-line-num old_line" data-linenumber="2648" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2648
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<td class="diff-line-num new_line" data-linenumber="2652" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2652
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<pre style="margin: 0;"> <span id="LC2652" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">q</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tr_lefts</span><span class="p">,</span> <span class="n" style="color: #333;">r</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">querystarts</span><span class="p">,</span> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">queryends</span><span class="p">,</span> <span class="n" style="color: #333;">t</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">adjustments</span><span class="p">;</span> <span class="n" style="color: #333;">q</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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2649
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<td class="diff-line-num new_line" data-linenumber="2653" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2653
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<pre style="margin: 0;"> <span id="LC2653" class="line" lang="c"> <span class="n" style="color: #333;">q</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Uintlist_next</span><span class="p">(</span><span class="n" style="color: #333;">q</span><span class="p">),</span> <span class="n" style="color: #333;">r</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Intlist_next</span><span class="p">(</span><span class="n" style="color: #333;">r</span><span class="p">),</span> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Intlist_next</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">))</span> <span class="p">{</span></span>
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2650
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2654
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<pre style="margin: 0;"> <span id="LC2654" class="line" lang="c"> <span class="n" style="color: #333;">transcript_diag</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Uintlist_head</span><span class="p">(</span><span class="n" style="color: #333;">q</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">troffset</span><span class="p">;</span></span>
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2651
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2655
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<pre style="margin: 0;"> <span id="LC2655" class="line" lang="c"></span>
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2652
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2656
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<pre style="margin: 0;"> <span id="LC2656" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Find initial exonpos */</span></span>
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2653
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<pre style="margin: 0;">-<span id="LC2653" class="line" lang="c"> <span class="n" style="color: #333;">abortp</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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2654
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2657
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<pre style="margin: 0;"> <span id="LC2657" class="line" lang="c"> <span class="n" style="color: #333;">queryend</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Intlist_head</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">);</span> <span class="cm" style="color: #998; font-style: italic;">/* tminus: compute from queryend to querystart */</span></span>
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2655
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2658
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<pre style="margin: 0;"> <span id="LC2658" class="line" lang="c"> <span class="n" style="color: #333;">querystart</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Intlist_head</span><span class="p">(</span><span class="n" style="color: #333;">r</span><span class="p">);</span></span>
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2656
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2659
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<pre style="margin: 0;"> <span id="LC2659" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</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;">Analyzing query %d..%d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">querystart</span><span class="p">,</span><span class="n" style="color: #333;">queryend</span><span class="p">));</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2764" style="width: 35px; color: rgba(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="2767" style="width: 35px; color: rgba(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">@@ -2764,7 +2767,7 @@ search_transcriptome_complete (Path_T **tplus_gplus_paths, int *n_tplus_gplus,</td>
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2764
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2767
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<pre style="margin: 0;"> <span id="LC2767" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">abortp</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">)</span> <span class="p">{</span></span>
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2765
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2768
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<pre style="margin: 0;"> <span id="LC2768" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Skip */</span></span>
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2766
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<td class="diff-line-num new_line" data-linenumber="2769" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2769
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<pre style="margin: 0;"> <span id="LC2769" class="line" lang="c"> <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="cm" style="color: #998; font-style: italic;">/*len <= nindels ||*/</span><span class="n" style="color: #333;">exon_residual</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">nindels</span><span class="p">)</span> <span class="p">{</span></span>
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2767
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<pre style="margin: 0;">-<span id="LC2767" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"ABORTING BECAUSE INDEL OVERLAPS SPLICE SITE</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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2770
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<pre style="margin: 0;">+<span id="LC2770" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"ABORTING BECAUSE INDEL OVERLAPS SPLICE SITE<span class="idiff left right"> (4)</span></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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2768
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2771
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<pre style="margin: 0;"> <span id="LC2771" class="line" lang="c"> <span class="n" style="color: #333;">abortp</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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2769
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2772
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<pre style="margin: 0;"> <span id="LC2772" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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2770
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2773
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<pre style="margin: 0;"> <span id="LC2773" class="line" lang="c"> <span class="n" style="color: #333;">gaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Intlist_push</span><span class="p">(</span><span class="n" style="color: #333;">gaps</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;">adj</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2873" style="width: 35px; color: rgba(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="2876" style="width: 35px; color: rgba(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">@@ -2873,6 +2876,7 @@ search_transcriptome_ends (Path_T **tplus_gplus_paths, int *n_tplus_gplus,</td>
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2873
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2876
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<pre style="margin: 0;"> <span id="LC2876" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifdef DEBUG2</span></span>
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2874
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2877
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<pre style="margin: 0;"> <span id="LC2877" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">trend</span><span class="p">;</span></span>
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2875
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2878
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<pre style="margin: 0;"> <span id="LC2878" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">allocp</span><span class="p">;</span></span>
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2879
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<pre style="margin: 0;">+<span id="LC2879" class="line" lang="c"> <span class="n" style="color: #333;">Univcoord_T</span> <span class="n" style="color: #333;">left</span><span class="p">;</span></span>
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2876
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2880
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<pre style="margin: 0;"> <span id="LC2880" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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2877
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2881
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<pre style="margin: 0;"> <span id="LC2881" class="line" lang="c"> <span class="n" style="color: #333;">Chrpos_T</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">exonstarts</span><span class="p">,</span> <span class="n" style="color: #333;">genomicpos</span><span class="p">,</span> <span class="n" style="color: #333;">chrlength</span><span class="p">;</span></span>
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2878
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2882
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<pre style="margin: 0;"> <span id="LC2882" class="line" lang="c"> <span class="n" style="color: #333;">Univcoord_T</span> <span class="n" style="color: #333;">alignstart</span><span class="p">,</span> <span class="n" style="color: #333;">alignend</span><span class="p">,</span> <span class="n" style="color: #333;">chroffset</span><span class="p">,</span> <span class="n" style="color: #333;">chrhigh</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2958" style="width: 35px; color: rgba(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">@@ -2954,7 +2958,7 @@ search_transcriptome_ends (Path_T **tplus_gplus_paths, int *n_tplus_gplus,</td>
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2954
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2958
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<pre style="margin: 0;"> <span id="LC2958" class="line" lang="c"> <span class="n" style="color: #333;">pos5</span><span class="p">,</span><span class="n" style="color: #333;">pos3</span><span class="p">,</span><span class="cm" style="color: #998; font-style: italic;">/*plusp*/</span><span class="nb" style="color: #0086b3;">true</span><span class="p">,</span><span class="cm" style="color: #998; font-style: italic;">/*genestrand*/</span><span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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2955
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2959
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<pre style="margin: 0;"> <span id="LC2959" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">nmismatches</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">nmismatches_allowed</span><span class="p">)</span> <span class="p">{</span></span>
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2956
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2960
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<pre style="margin: 0;"> <span id="LC2960" class="line" lang="c"> <span class="n" style="color: #333;">debug2a</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">" => nmismatches %d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">nmismatches</span><span class="p">));</span></span>
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2957
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<pre style="margin: 0;">-<span id="LC2957" class="line" lang="c"> <span class="n" style="color: #333;">total_nmatches</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left right">querylength</span></span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">nmismatches</span><span class="p">;</span></span>
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2961
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<pre style="margin: 0;">+<span id="LC2961" class="line" lang="c"> <span class="n" style="color: #333;">total_nmatches</span> <span class="o" style="font-weight: 600;">=</span> <span class="p"><span class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">pos3</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pos5</span></span><span class="p"><span class="idiff right">)</span></span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">nmismatches</span><span class="p">;</span></span>
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2958
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2962
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<pre style="margin: 0;"> <span id="LC2962" class="line" lang="c"></span>
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2959
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2963
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<pre style="margin: 0;"> <span id="LC2963" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Should replace with a rank/select structure */</span></span>
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2960
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2964
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<pre style="margin: 0;"> <span id="LC2964" class="line" lang="c"> <span class="n" style="color: #333;">abortp</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2976" style="width: 35px; color: rgba(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="2980" style="width: 35px; color: rgba(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">@@ -2976,9 +2980,9 @@ search_transcriptome_ends (Path_T **tplus_gplus_paths, int *n_tplus_gplus,</td>
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2976
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2980
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<pre style="margin: 0;"> <span id="LC2980" class="line" lang="c"> </span>
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2977
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2981
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<pre style="margin: 0;"> <span id="LC2981" class="line" lang="c"> <span class="n" style="color: #333;">endpoints</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">Uintlist_T</span><span class="p">)</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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2978
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2982
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<pre style="margin: 0;"> <span id="LC2982" class="line" lang="c"> <span class="n" style="color: #333;">gaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">Intlist_T</span><span class="p">)</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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2983
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<pre style="margin: 0;">+<span id="LC2983" class="line" lang="c"> <span class="n" style="color: #333;">abortp</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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2979
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2984
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<pre style="margin: 0;"> <span id="LC2984" class="line" lang="c"> </span>
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2980
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2985
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<pre style="margin: 0;"> <span id="LC2985" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Find initial exonpos */</span></span>
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2981
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<pre style="margin: 0;">-<span id="LC2981" class="line" lang="c"> <span class="n" style="color: #333;">abortp</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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2982
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2986
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<pre style="margin: 0;"> <span id="LC2986" class="line" lang="c"> <span class="n" style="color: #333;">querystart</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/* tplus: compute from querystart to queryend */</span></span>
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2983
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2987
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<pre style="margin: 0;"> <span id="LC2987" class="line" lang="c"> <span class="n" style="color: #333;">queryend</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">querylength</span><span class="p">;</span></span>
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2984
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2988
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<pre style="margin: 0;"> <span id="LC2988" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</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;">Analyzing query %d..%d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">querystart</span><span class="p">,</span><span class="n" style="color: #333;">queryend</span><span class="p">));</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="3106" style="width: 35px; color: rgba(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">@@ -3102,9 +3106,9 @@ search_transcriptome_ends (Path_T **tplus_gplus_paths, int *n_tplus_gplus,</td>
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3102
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3106
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<pre style="margin: 0;"> <span id="LC3106" class="line" lang="c"> </span>
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3103
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<td class="diff-line-num new_line" data-linenumber="3107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3107
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<pre style="margin: 0;"> <span id="LC3107" class="line" lang="c"> <span class="n" style="color: #333;">endpoints</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">Uintlist_T</span><span class="p">)</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="3104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3104
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<td class="diff-line-num new_line" data-linenumber="3108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3108
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<pre style="margin: 0;"> <span id="LC3108" class="line" lang="c"> <span class="n" style="color: #333;">gaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">Intlist_T</span><span class="p">)</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3109
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<pre style="margin: 0;">+<span id="LC3109" class="line" lang="c"> <span class="n" style="color: #333;">abortp</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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3105
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3110
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<pre style="margin: 0;"> <span id="LC3110" class="line" lang="c"> </span>
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3106
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<td class="diff-line-num new_line" data-linenumber="3111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3111
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<pre style="margin: 0;"> <span id="LC3111" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Find initial exonpos */</span></span>
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3107
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<td class="diff-line-num new_line old" data-linenumber="3112" 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="LC3107" class="line" lang="c"> <span class="n" style="color: #333;">abortp</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="3108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3108
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<td class="diff-line-num new_line" data-linenumber="3112" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3112
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<pre style="margin: 0;"> <span id="LC3112" class="line" lang="c"> <span class="n" style="color: #333;">querystart</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/* tplus: compute from querystart to queryend */</span></span>
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3109
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<td class="diff-line-num new_line" data-linenumber="3113" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3113
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<pre style="margin: 0;"> <span id="LC3113" class="line" lang="c"> <span class="n" style="color: #333;">queryend</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">querylength</span><span class="p">;</span></span>
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3110
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3114
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<pre style="margin: 0;"> <span id="LC3114" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</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;">Analyzing query %d..%d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">querystart</span><span class="p">,</span><span class="n" style="color: #333;">queryend</span><span class="p">));</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3258" style="width: 35px; color: rgba(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="3262" style="width: 35px; color: rgba(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">@@ -3258,11 +3262,13 @@ search_transcriptome_ends (Path_T **tplus_gplus_paths, int *n_tplus_gplus,</td>
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3258
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<td class="diff-line-num new_line" data-linenumber="3262" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3262
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<pre style="margin: 0;"> <span id="LC3262" class="line" lang="c"> <span class="n" style="color: #333;">pos3</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">tr_univdiagonal</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">transcriptomelength</span><span class="p">)</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">querylength</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="p">(</span><span class="n" style="color: #333;">transcriptomelength</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">tr_left</span><span class="p">);</span></span>
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3259
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3263
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<pre style="margin: 0;"> <span id="LC3263" class="line" lang="c"></span>
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3260
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<td class="diff-line-num new_line" data-linenumber="3264" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3264
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<pre style="margin: 0;"> <span id="LC3264" class="line" lang="c"> <span class="n" style="color: #333;">debug2a</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"ULTRAFAST MINUS DIAGONAL %u</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">tminus_diagpairs</span><span class="p">[</span><span class="n" style="color: #333;">k</span><span class="p">]));</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3265" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3265
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<pre style="margin: 0;">+<span id="LC3265" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Verified parameters to Genome_count_mismatches_substring */</span></span>
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3261
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<td class="diff-line-num new_line" data-linenumber="3266" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3266
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<pre style="margin: 0;"> <span id="LC3266" class="line" lang="c"> <span class="n" style="color: #333;">nmismatches</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Genome_count_mismatches_substring</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">ref_nmismatches</span><span class="p">,</span><span class="n" style="color: #333;">transcriptomebits</span><span class="p">,</span><span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span><span class="n" style="color: #333;">query_compress_rev</span><span class="p">,</span><span class="n" style="color: #333;">tr_left</span><span class="p">,</span></span>
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3262
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<td class="diff-line-num new_line" data-linenumber="3267" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3267
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<pre style="margin: 0;"> <span id="LC3267" class="line" lang="c"> <span class="n" style="color: #333;">pos5</span><span class="p">,</span><span class="n" style="color: #333;">pos3</span><span class="p">,</span><span class="cm" style="color: #998; font-style: italic;">/*plusp*/</span><span class="nb" style="color: #0086b3;">false</span><span class="p">,</span><span class="cm" style="color: #998; font-style: italic;">/*genestrand*/</span><span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3268" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3268
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<pre style="margin: 0;">+<span id="LC3268" class="line" lang="c"> </span>
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3263
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<td class="diff-line-num new_line" data-linenumber="3269" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3269
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<pre style="margin: 0;"> <span id="LC3269" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">nmismatches</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">nmismatches_allowed</span><span class="p">)</span> <span class="p">{</span></span>
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3264
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<td class="diff-line-num new_line" data-linenumber="3270" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3270
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<pre style="margin: 0;"> <span id="LC3270" class="line" lang="c"> <span class="n" style="color: #333;">debug2a</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">" => nmismatches %d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">nmismatches</span><span class="p">));</span></span>
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3265
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<pre style="margin: 0;">-<span id="LC3265" class="line" lang="c"> <span class="n" style="color: #333;">total_nmatches</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left right">querylength</span></span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">nmismatches</span><span class="p">;</span></span>
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3271
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<pre style="margin: 0;">+<span id="LC3271" class="line" lang="c"> <span class="n" style="color: #333;">total_nmatches</span> <span class="o" style="font-weight: 600;">=</span> <span class="p"><span class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">pos3</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">pos5</span></span><span class="p"><span class="idiff right">)</span></span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">nmismatches</span><span class="p">;</span></span>
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3266
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3272
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<pre style="margin: 0;"> <span id="LC3272" class="line" lang="c"></span>
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3267
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3273
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<pre style="margin: 0;"> <span id="LC3273" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Should replace with a rank/select structure */</span></span>
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3268
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3274
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<pre style="margin: 0;"> <span id="LC3274" class="line" lang="c"> <span class="n" style="color: #333;">abortp</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="3290" style="width: 35px; color: rgba(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">@@ -3284,9 +3290,9 @@ search_transcriptome_ends (Path_T **tplus_gplus_paths, int *n_tplus_gplus,</td>
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3284
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3290
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<pre style="margin: 0;"> <span id="LC3290" class="line" lang="c"> </span>
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3285
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3291
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<pre style="margin: 0;"> <span id="LC3291" class="line" lang="c"> <span class="n" style="color: #333;">endpoints</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">Uintlist_T</span><span class="p">)</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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3286
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3292
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<pre style="margin: 0;"> <span id="LC3292" class="line" lang="c"> <span class="n" style="color: #333;">gaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">Intlist_T</span><span class="p">)</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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3293
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<pre style="margin: 0;">+<span id="LC3293" class="line" lang="c"> <span class="n" style="color: #333;">abortp</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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3287
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3294
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<pre style="margin: 0;"> <span id="LC3294" class="line" lang="c"> </span>
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3288
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3295
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<pre style="margin: 0;"> <span id="LC3295" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Find initial exonpos */</span></span>
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3289
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<pre style="margin: 0;">-<span id="LC3289" class="line" lang="c"> <span class="n" style="color: #333;">abortp</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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3290
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3296
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<pre style="margin: 0;"> <span id="LC3296" class="line" lang="c"> <span class="n" style="color: #333;">queryend</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">querylength</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/* tminus: compute from queryend to querystart */</span></span>
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3291
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3297
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<pre style="margin: 0;"> <span id="LC3297" class="line" lang="c"> <span class="n" style="color: #333;">querystart</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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3292
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3298
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<pre style="margin: 0;"> <span id="LC3298" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</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;">Analyzing query %d..%d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">querystart</span><span class="p">,</span><span class="n" style="color: #333;">queryend</span><span class="p">));</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3410" style="width: 35px; color: rgba(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="3416" style="width: 35px; color: rgba(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">@@ -3410,9 +3416,9 @@ search_transcriptome_ends (Path_T **tplus_gplus_paths, int *n_tplus_gplus,</td>
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3410
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3416
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<pre style="margin: 0;"> <span id="LC3416" class="line" lang="c"> </span>
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3411
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3417
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<pre style="margin: 0;"> <span id="LC3417" class="line" lang="c"> <span class="n" style="color: #333;">endpoints</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">Uintlist_T</span><span class="p">)</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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3412
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3418
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<pre style="margin: 0;"> <span id="LC3418" class="line" lang="c"> <span class="n" style="color: #333;">gaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">Intlist_T</span><span class="p">)</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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3419
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<pre style="margin: 0;">+<span id="LC3419" class="line" lang="c"> <span class="n" style="color: #333;">abortp</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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3413
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3420
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<pre style="margin: 0;"> <span id="LC3420" class="line" lang="c"> </span>
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3414
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<td class="diff-line-num new_line" data-linenumber="3421" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3421
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<pre style="margin: 0;"> <span id="LC3421" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Find initial exonpos */</span></span>
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3415
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<pre style="margin: 0;">-<span id="LC3415" class="line" lang="c"> <span class="n" style="color: #333;">abortp</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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3416
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3422
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<pre style="margin: 0;"> <span id="LC3422" class="line" lang="c"> <span class="n" style="color: #333;">queryend</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">querylength</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/* tminus: compute from queryend to querystart */</span></span>
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<td class="diff-line-num old_line" data-linenumber="3417" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3417
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3423
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<pre style="margin: 0;"> <span id="LC3423" class="line" lang="c"> <span class="n" style="color: #333;">querystart</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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3418
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3424
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<pre style="margin: 0;"> <span id="LC3424" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</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;">Analyzing query %d..%d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">querystart</span><span class="p">,</span><span class="n" style="color: #333;">queryend</span><span class="p">));</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3589" style="width: 35px; color: rgba(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="3595" style="width: 35px; color: rgba(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">@@ -3589,475 +3595,480 @@ search_transcriptome_ends (Path_T **tplus_gplus_paths, int *n_tplus_gplus,</td>
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3589
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3595
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<pre style="margin: 0;"> <span id="LC3595" class="line" lang="c"> <span class="n" style="color: #333;">adj</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="p">(</span><span class="n" style="color: #333;">tr_univdiagonala</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">tr_univdiagonalb</span><span class="p">);</span></span>
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3590
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<td class="diff-line-num new_line" data-linenumber="3596" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3596
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<pre style="margin: 0;"> <span id="LC3596" class="line" lang="c"> <span class="n" style="color: #333;">debug2a</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"Setting b first, a second, adj %d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">adj</span><span class="p">));</span></span>
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<td class="diff-line-num old_line" data-linenumber="3591" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3591
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<td class="diff-line-num new_line" data-linenumber="3597" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3597
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<pre style="margin: 0;"> <span id="LC3597" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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3598
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<pre style="margin: 0;">+<span id="LC3598" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Read does not extend to the ends, so this method is not applicable */</span></span>
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3592
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3599
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<pre style="margin: 0;"> <span id="LC3599" class="line" lang="c"> <span class="n" style="color: #333;">adj</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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3593
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3600
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<pre style="margin: 0;"> <span id="LC3600" class="line" lang="c"> <span class="p">}</span></span>
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3594
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3601
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<pre style="margin: 0;"> <span id="LC3601" class="line" lang="c"></span>
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3595
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<pre style="margin: 0;">-<span id="LC3595" class="line" lang="c"> <span class="n" style="color: #333;">abortp</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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3596
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<td class="diff-line-num new_line old" data-linenumber="3602" 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="LC3596" class="line" lang="c"> <span class="n" style="color: #333;">trnum</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Univ_IIT_get_trnum</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">troffset</span><span class="p">,</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">trhigh</span><span class="p">,</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">trlength</span><span class="p">,</span><span class="n" style="color: #333;">transcript_iit</span><span class="p">,</span><span class="cm" style="color: #998; font-style: italic;">/*low*/</span><span class="n" style="color: #333;">low0</span><span class="p">,</span><span class="cm" style="color: #998; font-style: italic;">/*high*/</span><span class="n" style="color: #333;">high0</span><span class="p">);</span></span>
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3597
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<pre style="margin: 0;">-<span id="LC3597" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"trnum is %d: %s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">trnum</span><span class="p">,</span><span class="n" style="color: #333;">Univ_IIT_label</span><span class="p">(</span><span class="n" style="color: #333;">transcript_iit</span><span class="p">,</span><span class="n" style="color: #333;">trnum</span><span class="p">,</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">allocp</span><span class="p">)));</span></span>
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3598
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<pre style="margin: 0;">-<span id="LC3598" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">chrnum</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Transcriptome_chrnum</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">transcript_genestrand</span><span class="p">,</span><span class="n" style="color: #333;">transcriptome</span><span class="p">,</span><span class="n" style="color: #333;">trnum</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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3599
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<pre style="margin: 0;">-<span id="LC3599" class="line" lang="c"> <span class="n" style="color: #333;">abortp</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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3600
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<pre style="margin: 0;">-<span id="LC3600" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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3601
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<pre style="margin: 0;">-<span id="LC3601" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">transcript_genestrand</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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3602
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<pre style="margin: 0;">-<span id="LC3602" class="line" lang="c"> <span class="n" style="color: #333;">want_lowest_coordinate_p</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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3603
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<pre style="margin: 0;">-<span id="LC3603" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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3604
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<pre style="margin: 0;">-<span id="LC3604" class="line" lang="c"> <span class="n" style="color: #333;">want_lowest_coordinate_p</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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3605
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<pre style="margin: 0;">-<span id="LC3605" class="line" lang="c"> <span class="p">}</span></span>
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3606
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<pre style="margin: 0;">-<span id="LC3606" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"trnum %d, transcript_genestrand %d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">trnum</span><span class="p">,</span><span class="n" style="color: #333;">transcript_genestrand</span><span class="p">));</span></span>
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3607
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<pre style="margin: 0;">-<span id="LC3607" class="line" lang="c"></span>
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3608
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<td class="diff-line-num new_line old" data-linenumber="3602" 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="LC3608" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">adj</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>
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<td class="diff-line-num old old_line" data-linenumber="3609" 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">
3609
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<td class="diff-line-num new_line old" data-linenumber="3602" 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="LC3609" class="line" lang="c"> <span class="p">(</span><span class="n" style="color: #333;">indel_pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Indel_resolve_middle_deletion</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">best_nmismatches_i</span><span class="p">,</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">best_nmismatches_j</span><span class="p">,</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3610" 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">
3610
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<pre style="margin: 0;">-<span id="LC3610" class="line" lang="c"> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">best_ref_nmismatches_i</span><span class="p">,</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">best_ref_nmismatches_j</span><span class="p">,</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3611" 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">
3611
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<td class="diff-line-num new_line old" data-linenumber="3602" 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="LC3611" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/*left*/</span><span class="n" style="color: #333;">tr_left0</span><span class="p">,</span><span class="cm" style="color: #998; font-style: italic;">/*indels*/</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">adj</span><span class="p">,</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3612" 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">
3612
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<td class="diff-line-num new_line old" data-linenumber="3602" 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="LC3612" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/*mismatch_positions_left*/</span><span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span><span class="cm" style="color: #998; font-style: italic;">/*nmismatches_left*/</span><span class="mi" style="color: #099;">0</span><span class="p">,</span></span>
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3613
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<td class="diff-line-num new_line old" data-linenumber="3602" 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="LC3613" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/*mismatch_positions_right*/</span><span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span><span class="cm" style="color: #998; font-style: italic;">/*nmismatches_right*/</span><span class="mi" style="color: #099;">0</span><span class="p">,</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3614" 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">
3614
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<td class="diff-line-num new_line old" data-linenumber="3602" 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="LC3614" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/*ome*/</span><span class="n" style="color: #333;">transcriptomebits</span><span class="p">,</span><span class="cm" style="color: #998; font-style: italic;">/*ome_alt*/</span><span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span><span class="n" style="color: #333;">query_compress_fwd</span><span class="p">,</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3615" 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">
3615
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<td class="diff-line-num new_line old" data-linenumber="3602" 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="LC3615" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/*querystart*/</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="cm" style="color: #998; font-style: italic;">/*queryend*/</span><span class="n" style="color: #333;">querylength</span><span class="p">,</span><span class="n" style="color: #333;">querylength</span><span class="p">,</span></span>
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3616
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<td class="diff-line-num new_line old" data-linenumber="3602" 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="LC3616" class="line" lang="c"> <span class="n" style="color: #333;">nmismatches_allowed</span><span class="p">,</span><span class="cm" style="color: #998; font-style: italic;">/*plusp*/</span><span class="nb" style="color: #0086b3;">true</span><span class="p">,</span><span class="cm" style="color: #998; font-style: italic;">/*genestrand*/</span><span class="mi" style="color: #099;">0</span><span class="p">,</span></span>
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3617
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<pre style="margin: 0;">-<span id="LC3617" class="line" lang="c"> <span class="n" style="color: #333;">want_lowest_coordinate_p</span><span class="p">))</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3618" 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">
3618
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<pre style="margin: 0;">-<span id="LC3618" class="line" lang="c"> <span class="n" style="color: #333;">ninserts</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3619" 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">
3619
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<pre style="margin: 0;">-<span id="LC3619" class="line" lang="c"> <span class="n" style="color: #333;">nindels</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">adj</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3620" 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">
3620
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<pre style="margin: 0;">-<span id="LC3620" class="line" lang="c"> <span class="n" style="color: #333;">total_nmatches</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">querylength</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">best_nmismatches_i</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">best_nmismatches_j</span><span class="p">;</span></span>
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3621
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<td class="diff-line-num new_line old" data-linenumber="3602" 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="LC3621" class="line" lang="c"> <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;">adj</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>
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3622
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<pre style="margin: 0;">-<span id="LC3622" class="line" lang="c"> <span class="p">(</span><span class="n" style="color: #333;">indel_pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Indel_resolve_middle_insertion</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">best_nmismatches_i</span><span class="p">,</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">best_nmismatches_j</span><span class="p">,</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3623" 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">
3623
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<td class="diff-line-num new_line old" data-linenumber="3602" 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="LC3623" class="line" lang="c"> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">best_ref_nmismatches_i</span><span class="p">,</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">best_ref_nmismatches_j</span><span class="p">,</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3624" 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">
3624
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<td class="diff-line-num new_line old" data-linenumber="3602" 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="LC3624" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/*left*/</span><span class="n" style="color: #333;">tr_left0</span><span class="p">,</span><span class="cm" style="color: #998; font-style: italic;">/*indels*/</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">adj</span><span class="p">,</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3625" 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">
3625
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<td class="diff-line-num new_line old" data-linenumber="3602" 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="LC3625" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/*mismatch_positions_left*/</span><span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span><span class="cm" style="color: #998; font-style: italic;">/*nmismatches_left*/</span><span class="mi" style="color: #099;">0</span><span class="p">,</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3626" 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">
3626
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<td class="diff-line-num new_line old" data-linenumber="3602" 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="LC3626" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/*mismatch_positions_right*/</span><span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span><span class="cm" style="color: #998; font-style: italic;">/*nmismatches_right*/</span><span class="mi" style="color: #099;">0</span><span class="p">,</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3627" 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">
3627
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<td class="diff-line-num new_line old" data-linenumber="3602" 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="LC3627" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/*ome*/</span><span class="n" style="color: #333;">transcriptomebits</span><span class="p">,</span><span class="cm" style="color: #998; font-style: italic;">/*ome_alt*/</span><span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span><span class="n" style="color: #333;">query_compress_fwd</span><span class="p">,</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3628" 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">
3628
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<td class="diff-line-num new_line old" data-linenumber="3602" 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="LC3628" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/*querystart*/</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="cm" style="color: #998; font-style: italic;">/*queryend*/</span><span class="n" style="color: #333;">querylength</span><span class="p">,</span><span class="n" style="color: #333;">querylength</span><span class="p">,</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3629" 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">
3629
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<td class="diff-line-num new_line old" data-linenumber="3602" 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="LC3629" class="line" lang="c"> <span class="n" style="color: #333;">nmismatches_allowed</span><span class="p">,</span><span class="cm" style="color: #998; font-style: italic;">/*plusp*/</span><span class="nb" style="color: #0086b3;">true</span><span class="p">,</span><span class="cm" style="color: #998; font-style: italic;">/*genestrand*/</span><span class="mi" style="color: #099;">0</span><span class="p">,</span></span>
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3630
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<td class="diff-line-num new_line old" data-linenumber="3602" 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="LC3630" class="line" lang="c"> <span class="n" style="color: #333;">want_lowest_coordinate_p</span><span class="p">))</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3631" 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">
3631
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<td class="diff-line-num new_line old" data-linenumber="3602" 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="LC3631" class="line" lang="c"> <span class="n" style="color: #333;">ninserts</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nindels</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">adj</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3632" 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">
3632
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<td class="diff-line-num new_line old" data-linenumber="3602" 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="LC3632" class="line" lang="c"> <span class="n" style="color: #333;">total_nmatches</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">querylength</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">best_nmismatches_i</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">best_nmismatches_j</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">ninserts</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3633" 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">
3633
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<td class="diff-line-num new_line old" data-linenumber="3602" 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="LC3633" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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3602
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<pre style="margin: 0;">+<span id="LC3602" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">adj</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3603" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3603
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<pre style="margin: 0;">+<span id="LC3603" class="line" lang="c"> <span class="n" style="color: #333;">trnum</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Univ_IIT_get_trnum</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">troffset</span><span class="p">,</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">trhigh</span><span class="p">,</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">trlength</span><span class="p">,</span><span class="n" style="color: #333;">transcript_iit</span><span class="p">,</span><span class="cm" style="color: #998; font-style: italic;">/*low*/</span><span class="n" style="color: #333;">low0</span><span class="p">,</span><span class="cm" style="color: #998; font-style: italic;">/*high*/</span><span class="n" style="color: #333;">high0</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3604" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3604
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<pre style="margin: 0;">+<span id="LC3604" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"trnum is %d: %s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">trnum</span><span class="p">,</span><span class="n" style="color: #333;">Univ_IIT_label</span><span class="p">(</span><span class="n" style="color: #333;">transcript_iit</span><span class="p">,</span><span class="n" style="color: #333;">trnum</span><span class="p">,</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">allocp</span><span class="p">)));</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3605" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3605
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<pre style="margin: 0;">+<span id="LC3605" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">chrnum</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Transcriptome_chrnum</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">transcript_genestrand</span><span class="p">,</span><span class="n" style="color: #333;">transcriptome</span><span class="p">,</span><span class="n" style="color: #333;">trnum</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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3634
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<td class="diff-line-num new_line" data-linenumber="3606" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3606
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<pre style="margin: 0;"> <span id="LC3606" class="line" lang="c"> <span class="n" style="color: #333;">adj</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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3635
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<td class="diff-line-num new_line old" data-linenumber="3607" 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="LC3635" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3607" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3607
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<pre style="margin: 0;">+<span id="LC3607" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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3608
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<pre style="margin: 0;">+<span id="LC3608" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">transcript_genestrand</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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3609
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<pre style="margin: 0;">+<span id="LC3609" class="line" lang="c"> <span class="n" style="color: #333;">want_lowest_coordinate_p</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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3610
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<pre style="margin: 0;">+<span id="LC3610" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3611" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3611
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<pre style="margin: 0;">+<span id="LC3611" class="line" lang="c"> <span class="n" style="color: #333;">want_lowest_coordinate_p</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3612" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3612
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<pre style="margin: 0;">+<span id="LC3612" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3613" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3613
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<pre style="margin: 0;">+<span id="LC3613" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"trnum %d, transcript_genestrand %d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">trnum</span><span class="p">,</span><span class="n" style="color: #333;">transcript_genestrand</span><span class="p">));</span></span>
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3636
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3614
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<pre style="margin: 0;"> <span id="LC3614" class="line" lang="c"></span>
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3637
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<td class="diff-line-num new_line old" data-linenumber="3615" 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="LC3637" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">adj</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3638" 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">
3638
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<td class="diff-line-num new_line old" data-linenumber="3615" 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="LC3638" class="line" lang="c"> <span class="n" style="color: #333;">nexons</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Transcriptome_exons</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">exonbounds</span><span class="p">,</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">exonstarts</span><span class="p">,</span><span class="n" style="color: #333;">transcriptome</span><span class="p">,</span><span class="n" style="color: #333;">trnum</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3639" 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">
3639
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<td class="diff-line-num new_line old" data-linenumber="3615" 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="LC3639" class="line" lang="c"> <span class="n" style="color: #333;">Univ_IIT_interval_bounds</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">chroffset</span><span class="p">,</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">chrhigh</span><span class="p">,</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">chrlength</span><span class="p">,</span><span class="n" style="color: #333;">chromosome_iit</span><span class="p">,</span><span class="n" style="color: #333;">chrnum</span><span class="p">,</span><span class="n" style="color: #333;">circular_typeint</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3615" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3615
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<pre style="margin: 0;">+<span id="LC3615" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">adj</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>
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<td class="diff-line-num new new_line" data-linenumber="3616" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3616
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<pre style="margin: 0;">+<span id="LC3616" class="line" lang="c"> <span class="p">(</span><span class="n" style="color: #333;">indel_pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Indel_resolve_middle_deletion</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">best_nmismatches_i</span><span class="p">,</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">best_nmismatches_j</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3617" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3617
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<pre style="margin: 0;">+<span id="LC3617" class="line" lang="c"> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">best_ref_nmismatches_i</span><span class="p">,</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">best_ref_nmismatches_j</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3618" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3618
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<pre style="margin: 0;">+<span id="LC3618" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/*left*/</span><span class="n" style="color: #333;">tr_left0</span><span class="p">,</span><span class="cm" style="color: #998; font-style: italic;">/*indels*/</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">adj</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3619" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3619
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<pre style="margin: 0;">+<span id="LC3619" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/*mismatch_positions_left*/</span><span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span><span class="cm" style="color: #998; font-style: italic;">/*nmismatches_left*/</span><span class="mi" style="color: #099;">0</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3620" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3620
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<pre style="margin: 0;">+<span id="LC3620" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/*mismatch_positions_right*/</span><span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span><span class="cm" style="color: #998; font-style: italic;">/*nmismatches_right*/</span><span class="mi" style="color: #099;">0</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3621" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3621
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<pre style="margin: 0;">+<span id="LC3621" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/*ome*/</span><span class="n" style="color: #333;">transcriptomebits</span><span class="p">,</span><span class="cm" style="color: #998; font-style: italic;">/*ome_alt*/</span><span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span><span class="n" style="color: #333;">query_compress_fwd</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3622" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3622
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<pre style="margin: 0;">+<span id="LC3622" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/*querystart*/</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="cm" style="color: #998; font-style: italic;">/*queryend*/</span><span class="n" style="color: #333;">querylength</span><span class="p">,</span><span class="n" style="color: #333;">querylength</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3623" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3623
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<pre style="margin: 0;">+<span id="LC3623" class="line" lang="c"> <span class="n" style="color: #333;">nmismatches_allowed</span><span class="p">,</span><span class="cm" style="color: #998; font-style: italic;">/*plusp*/</span><span class="nb" style="color: #0086b3;">true</span><span class="p">,</span><span class="cm" style="color: #998; font-style: italic;">/*genestrand*/</span><span class="mi" style="color: #099;">0</span><span class="p">,</span></span>
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3624
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<pre style="margin: 0;">+<span id="LC3624" class="line" lang="c"> <span class="n" style="color: #333;">want_lowest_coordinate_p</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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3625
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<pre style="margin: 0;">+<span id="LC3625" class="line" lang="c"> <span class="n" style="color: #333;">ninserts</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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3626
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<pre style="margin: 0;">+<span id="LC3626" class="line" lang="c"> <span class="n" style="color: #333;">nindels</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">adj</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3627" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3627
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<pre style="margin: 0;">+<span id="LC3627" class="line" lang="c"> <span class="n" style="color: #333;">total_nmatches</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">querylength</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">best_nmismatches_i</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">best_nmismatches_j</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3628" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3628
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<pre style="margin: 0;">+<span id="LC3628" class="line" lang="c"> <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;">adj</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>
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<td class="diff-line-num new new_line" data-linenumber="3629" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3629
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<pre style="margin: 0;">+<span id="LC3629" class="line" lang="c"> <span class="p">(</span><span class="n" style="color: #333;">indel_pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Indel_resolve_middle_insertion</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">best_nmismatches_i</span><span class="p">,</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">best_nmismatches_j</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3630" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3630
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<pre style="margin: 0;">+<span id="LC3630" class="line" lang="c"> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">best_ref_nmismatches_i</span><span class="p">,</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">best_ref_nmismatches_j</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3631" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3631
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<pre style="margin: 0;">+<span id="LC3631" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/*left*/</span><span class="n" style="color: #333;">tr_left0</span><span class="p">,</span><span class="cm" style="color: #998; font-style: italic;">/*indels*/</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">adj</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3632" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3632
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<pre style="margin: 0;">+<span id="LC3632" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/*mismatch_positions_left*/</span><span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span><span class="cm" style="color: #998; font-style: italic;">/*nmismatches_left*/</span><span class="mi" style="color: #099;">0</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3633" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3633
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<pre style="margin: 0;">+<span id="LC3633" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/*mismatch_positions_right*/</span><span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span><span class="cm" style="color: #998; font-style: italic;">/*nmismatches_right*/</span><span class="mi" style="color: #099;">0</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3634" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3634
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<pre style="margin: 0;">+<span id="LC3634" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/*ome*/</span><span class="n" style="color: #333;">transcriptomebits</span><span class="p">,</span><span class="cm" style="color: #998; font-style: italic;">/*ome_alt*/</span><span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span><span class="n" style="color: #333;">query_compress_fwd</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3635" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3635
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<pre style="margin: 0;">+<span id="LC3635" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/*querystart*/</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="cm" style="color: #998; font-style: italic;">/*queryend*/</span><span class="n" style="color: #333;">querylength</span><span class="p">,</span><span class="n" style="color: #333;">querylength</span><span class="p">,</span></span>
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3636
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<pre style="margin: 0;">+<span id="LC3636" class="line" lang="c"> <span class="n" style="color: #333;">nmismatches_allowed</span><span class="p">,</span><span class="cm" style="color: #998; font-style: italic;">/*plusp*/</span><span class="nb" style="color: #0086b3;">true</span><span class="p">,</span><span class="cm" style="color: #998; font-style: italic;">/*genestrand*/</span><span class="mi" style="color: #099;">0</span><span class="p">,</span></span>
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3637
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<pre style="margin: 0;">+<span id="LC3637" class="line" lang="c"> <span class="n" style="color: #333;">want_lowest_coordinate_p</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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3638
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<pre style="margin: 0;">+<span id="LC3638" class="line" lang="c"> <span class="n" style="color: #333;">ninserts</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nindels</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">adj</span><span class="p">;</span></span>
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3639
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<pre style="margin: 0;">+<span id="LC3639" class="line" lang="c"> <span class="n" style="color: #333;">total_nmatches</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">querylength</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">best_nmismatches_i</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">best_nmismatches_j</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">ninserts</span><span class="p">;</span></span>
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3640
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<pre style="margin: 0;">+<span id="LC3640" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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3641
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<pre style="margin: 0;">+<span id="LC3641" class="line" lang="c"> <span class="n" style="color: #333;">adj</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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3642
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<pre style="margin: 0;">+<span id="LC3642" class="line" lang="c"> <span class="p">}</span></span>
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3643
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<pre style="margin: 0;">+<span id="LC3643" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC3644" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC3645" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC3641" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">transcript_genestrand</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="LC3642" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Case 1 ultrafast gap: tplus, gplus. transcript_plusp == true && transcript_genestrand > 0 */</span></span>
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<pre style="margin: 0;">-<span id="LC3643" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"Case 1 ultrafast gap: tplus, gplus</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="LC3644" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* sensedir = SENSE_FORWARD; */</span></span>
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<pre style="margin: 0;">-<span id="LC3645" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* plusp = true; */</span></span>
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<pre style="margin: 0;">+<span id="LC3646" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">adj</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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3647
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<pre style="margin: 0;">+<span id="LC3647" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Skip finding an indel */</span></span>
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3648
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<pre style="margin: 0;"> <span id="LC3648" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC3647" class="line" lang="c"> <span class="n" style="color: #333;">endpoints</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">Uintlist_T</span><span class="p">)</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC3648" class="line" lang="c"> <span class="n" style="color: #333;">gaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">Intlist_T</span><span class="p">)</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC3649" class="line" lang="c"> </span>
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<pre style="margin: 0;">-<span id="LC3650" class="line" lang="c"> <span class="n" style="color: #333;">transcript_diag0</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tr_left0</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">troffset</span><span class="p">;</span></span>
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3651
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<pre style="margin: 0;">-<span id="LC3651" class="line" lang="c"> <span class="n" style="color: #333;">transcript_diag1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tr_left1</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">troffset</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC3649" class="line" lang="c"> <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;">transcript_genestrand</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="LC3650" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Case 1 ultrafast gap: tplus, gplus. transcript_plusp == true && transcript_genestrand > 0 */</span></span>
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<pre style="margin: 0;">+<span id="LC3651" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"Case 1 ultrafast gap: tplus, gplus</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="LC3652" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC3653" class="line" lang="c"> <span class="n" style="color: #333;">abortp</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="LC3653" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* sensedir = SENSE_FORWARD; */</span></span>
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<pre style="margin: 0;">+<span id="LC3654" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* plusp = true; */</span></span>
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<pre style="margin: 0;"> <span id="LC3655" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC3655" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* first part */</span></span>
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<pre style="margin: 0;">-<span id="LC3656" class="line" lang="c"> <span class="n" style="color: #333;">tr_left</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tr_left0</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC3657" class="line" lang="c"> <span class="n" style="color: #333;">querystart</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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3658
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<pre style="margin: 0;">-<span id="LC3658" class="line" lang="c"> <span class="n" style="color: #333;">queryend</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">indel_pos</span><span class="p">;</span></span>
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3659
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<pre style="margin: 0;">-<span id="LC3659" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</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;">Analyzing query %d..%d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">querystart</span><span class="p">,</span><span class="n" style="color: #333;">queryend</span><span class="p">));</span></span>
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<pre style="margin: 0;">+<span id="LC3656" class="line" lang="c"> <span class="n" style="color: #333;">nexons</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Transcriptome_exons</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">exonbounds</span><span class="p">,</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">exonstarts</span><span class="p">,</span><span class="n" style="color: #333;">transcriptome</span><span class="p">,</span><span class="n" style="color: #333;">trnum</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC3657" class="line" lang="c"> <span class="n" style="color: #333;">Univ_IIT_interval_bounds</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">chroffset</span><span class="p">,</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">chrhigh</span><span class="p">,</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">chrlength</span><span class="p">,</span><span class="n" style="color: #333;">chromosome_iit</span><span class="p">,</span><span class="n" style="color: #333;">chrnum</span><span class="p">,</span><span class="n" style="color: #333;">circular_typeint</span><span class="p">);</span></span>
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3660
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<pre style="margin: 0;"> <span id="LC3658" class="line" lang="c"></span>
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3661
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<pre style="margin: 0;">-<span id="LC3661" class="line" lang="c"> <span class="n" style="color: #333;">overall_trstart</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">trstart</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">transcript_diag0</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">querystart</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/* tplus */</span></span>
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<pre style="margin: 0;">+<span id="LC3659" class="line" lang="c"> <span class="n" style="color: #333;">endpoints</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">Uintlist_T</span><span class="p">)</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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3660
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<pre style="margin: 0;">+<span id="LC3660" class="line" lang="c"> <span class="n" style="color: #333;">gaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">Intlist_T</span><span class="p">)</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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3661
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<pre style="margin: 0;">+<span id="LC3661" class="line" lang="c"> <span class="n" style="color: #333;">abortp</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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3662
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<pre style="margin: 0;">+<span id="LC3662" class="line" lang="c"> </span>
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3663
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<pre style="margin: 0;">+<span id="LC3663" class="line" lang="c"> <span class="n" style="color: #333;">transcript_diag0</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tr_left0</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">troffset</span><span class="p">;</span></span>
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3664
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<pre style="margin: 0;">+<span id="LC3664" class="line" lang="c"> <span class="n" style="color: #333;">transcript_diag1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tr_left1</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">troffset</span><span class="p">;</span></span>
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3665
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<pre style="margin: 0;">+<span id="LC3665" class="line" lang="c"> </span>
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3666
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<pre style="margin: 0;">+<span id="LC3666" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* first part */</span></span>
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3667
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<pre style="margin: 0;">+<span id="LC3667" class="line" lang="c"> <span class="n" style="color: #333;">tr_left</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tr_left0</span><span class="p">;</span></span>
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3668
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<pre style="margin: 0;">+<span id="LC3668" class="line" lang="c"> <span class="n" style="color: #333;">querystart</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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3669
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<pre style="margin: 0;">+<span id="LC3669" class="line" lang="c"> <span class="n" style="color: #333;">queryend</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">indel_pos</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC3670" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</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;">Analyzing query %d..%d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">querystart</span><span class="p">,</span><span class="n" style="color: #333;">queryend</span><span class="p">));</span></span>
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3671
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<pre style="margin: 0;">+<span id="LC3671" class="line" lang="c"> </span>
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3672
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<pre style="margin: 0;">+<span id="LC3672" class="line" lang="c"> <span class="n" style="color: #333;">overall_trstart</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">trstart</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">transcript_diag0</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">querystart</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/* tplus */</span></span>
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3662
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3673
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<pre style="margin: 0;"> <span id="LC3673" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifdef DEBUG2</span></span>
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3663
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<pre style="margin: 0;">-<span id="LC3663" class="line" lang="c"> <span class="idiff left right"> </span><span class="n" style="color: #333;">trend</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">transcript_diag0</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">queryend</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/* tplus */</span></span>
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3664
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<pre style="margin: 0;">-<span id="LC3664" class="line" lang="c"> <span class="idiff left right"> </span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"transcript_diag %d, trstart %d, trend %d, tr_left %u, adj %d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span></span>
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3665
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<pre style="margin: 0;">-<span id="LC3665" class="line" lang="c"> <span class="idiff left right"> </span><span class="n" style="color: #333;">transcript_diag0</span><span class="p">,</span><span class="n" style="color: #333;">trstart</span><span class="p">,</span><span class="n" style="color: #333;">trend</span><span class="p">,</span> <span class="n" style="color: #333;">tr_left</span><span class="p">,</span><span class="n" style="color: #333;">adj</span><span class="p">);</span></span>
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3674
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<pre style="margin: 0;">+<span id="LC3674" class="line" lang="c"> <span class="n" style="color: #333;">trend</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">transcript_diag0</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">queryend</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/* tplus */</span></span>
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3675
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<pre style="margin: 0;">+<span id="LC3675" class="line" lang="c"> <span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"transcript_diag %d, trstart %d, trend %d, tr_left %u, adj %d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span></span>
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3676
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<pre style="margin: 0;">+<span id="LC3676" class="line" lang="c"> <span class="n" style="color: #333;">transcript_diag0</span><span class="p">,</span><span class="n" style="color: #333;">trstart</span><span class="p">,</span><span class="n" style="color: #333;">trend</span><span class="p">,</span> <span class="n" style="color: #333;">tr_left</span><span class="p">,</span><span class="n" style="color: #333;">adj</span><span class="p">);</span></span>
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3666
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3677
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<pre style="margin: 0;"> <span id="LC3677" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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3667
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<pre style="margin: 0;">-<span id="LC3667" class="line" lang="c"></span>
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3668
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<pre style="margin: 0;">-<span id="LC3668" class="line" lang="c"> <span class="idiff left right"> </span><span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"Searching for exoni for trstart %d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">trstart</span><span class="p">));</span></span>
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3669
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<pre style="margin: 0;">-<span id="LC3669" class="line" lang="c"> <span class="idiff left right"> </span><span class="n" style="color: #333;">exoni</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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3678
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<pre style="margin: 0;">+<span id="LC3678" class="line" lang="c"> </span>
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3679
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<pre style="margin: 0;">+<span id="LC3679" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"Searching for exoni for trstart %d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">trstart</span><span class="p">));</span></span>
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3680
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<pre style="margin: 0;">+<span id="LC3680" class="line" lang="c"> <span class="n" style="color: #333;">exoni</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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3670
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3681
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<pre style="margin: 0;"> <span id="LC3681" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;">#if 0 && defined(HAVE_AVX2)</span></span>
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3671
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<pre style="margin: 0;">-<span id="LC3671" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> <span class="idiff left right"> </span>_trstart = _mm256_set1_epi32(trstart);</span></span>
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3672
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<pre style="margin: 0;">-<span id="LC3672" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> <span class="idiff left right"> </span>ptr = exonbounds;</span></span>
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3673
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<pre style="margin: 0;">-<span id="LC3673" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> <span class="idiff left right"> </span>_exonbounds = _mm256_loadu_si256((__m256i *) ptr);</span></span>
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3674
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<pre style="margin: 0;">-<span id="LC3674" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> <span class="idiff left right"> </span>_diff = _mm256_cmpgt_epi32(_exonbounds,_trstart);</span></span>
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3675
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<pre style="margin: 0;">-<span id="LC3675" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> <span class="idiff left right"> </span>while (all_zero_p(_diff)) {</span></span>
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3676
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<td class="diff-line-num new_line old" data-linenumber="3682" 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="LC3676" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> <span class="idiff left right"> </span>exoni += 8;</span></span>
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3677
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<pre style="margin: 0;">-<span id="LC3677" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> <span class="idiff left right"> </span>ptr += 8;</span></span>
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3678
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<pre style="margin: 0;">-<span id="LC3678" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> <span class="idiff left right"> </span>_exonbounds = _mm256_loadu_si256((__m256i *) ptr);</span></span>
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3679
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<pre style="margin: 0;">-<span id="LC3679" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> <span class="idiff left right"> </span>_diff = _mm256_cmpgt_epi32(_exonbounds,_trstart);</span></span>
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3680
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<pre style="margin: 0;">-<span id="LC3680" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> <span class="idiff left right"> </span>}</span></span>
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3681
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<pre style="margin: 0;">-<span id="LC3681" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> <span class="idiff left right"> </span>matchbits = _mm256_movemask_ps(_mm256_castsi256_ps(_diff));</span></span>
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3682
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<pre style="margin: 0;">-<span id="LC3682" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> <span class="idiff left right"> </span>exoni += count_trailing_zeroes_32(matchbits);</span></span>
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3682
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<pre style="margin: 0;">+<span id="LC3682" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> _trstart = _mm256_set1_epi32(trstart);</span></span>
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3683
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<pre style="margin: 0;">+<span id="LC3683" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> ptr = exonbounds;</span></span>
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3684
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<pre style="margin: 0;">+<span id="LC3684" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> _exonbounds = _mm256_loadu_si256((__m256i *) ptr);</span></span>
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3685
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<pre style="margin: 0;">+<span id="LC3685" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> _diff = _mm256_cmpgt_epi32(_exonbounds,_trstart);</span></span>
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3686
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<pre style="margin: 0;">+<span id="LC3686" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> while (all_zero_p(_diff)) {</span></span>
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3687
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<pre style="margin: 0;">+<span id="LC3687" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> <span class="idiff left right"> </span>exoni += 8;</span></span>
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3688
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<pre style="margin: 0;">+<span id="LC3688" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> <span class="idiff left right"> </span>ptr += 8;</span></span>
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3689
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<pre style="margin: 0;">+<span id="LC3689" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> <span class="idiff left right"> </span>_exonbounds = _mm256_loadu_si256((__m256i *) ptr);</span></span>
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3690
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<pre style="margin: 0;">+<span id="LC3690" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> <span class="idiff left right"> </span>_diff = _mm256_cmpgt_epi32(_exonbounds,_trstart);</span></span>
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3691
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<pre style="margin: 0;">+<span id="LC3691" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> }</span></span>
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3692
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<pre style="margin: 0;">+<span id="LC3692" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> matchbits = _mm256_movemask_ps(_mm256_castsi256_ps(_diff));</span></span>
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3693
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<pre style="margin: 0;">+<span id="LC3693" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> exoni += count_trailing_zeroes_32(matchbits);</span></span>
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3683
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3694
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<pre style="margin: 0;"> <span id="LC3694" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;">#elif</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">defined</span><span class="p">(</span><span class="n" style="color: #333;">HAVE_SSE2</span><span class="p">)</span></span>
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3684
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<pre style="margin: 0;">-<span id="LC3684" class="line" lang="c"> <span class="idiff left right"> </span><span class="n" style="color: #333;">_trstart</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_set1_epi32</span><span class="p">(</span><span class="n" style="color: #333;">trstart</span><span class="p">);</span></span>
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3685
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<pre style="margin: 0;">-<span id="LC3685" class="line" lang="c"> <span class="idiff left right"> </span><span class="n" style="color: #333;">ptr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">exonbounds</span><span class="p">;</span></span>
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3686
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<td class="diff-line-num new_line old" data-linenumber="3695" 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="LC3686" class="line" lang="c"> <span class="idiff left right"> </span><span class="n" style="color: #333;">_exonbounds</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_loadu_si128</span><span class="p">((</span><span class="n" style="color: #333;">__m128i</span> <span class="o" style="font-weight: 600;">*</span><span class="p">)</span> <span class="n" style="color: #333;">ptr</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3687" 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">
3687
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<td class="diff-line-num new_line old" data-linenumber="3695" 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="LC3687" class="line" lang="c"> <span class="idiff left right"> </span><span class="n" style="color: #333;">_diff</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_cmpgt_epi32</span><span class="p">(</span><span class="n" style="color: #333;">_exonbounds</span><span class="p">,</span><span class="n" style="color: #333;">_trstart</span><span class="p">);</span></span>
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3688
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<td class="diff-line-num new_line old" data-linenumber="3695" 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="LC3688" class="line" lang="c"> <span class="idiff left right"> </span><span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">all_zero_p</span><span class="p">(</span><span class="n" style="color: #333;">_diff</span><span class="p">))</span> <span class="p">{</span></span>
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3689
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<td class="diff-line-num new_line old" data-linenumber="3695" 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="LC3689" class="line" lang="c"> <span class="idiff left right"> </span><span class="n" style="color: #333;">exoni</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">4</span><span class="p">;</span></span>
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3690
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<td class="diff-line-num new_line old" data-linenumber="3695" 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="LC3690" class="line" lang="c"> <span class="idiff left right"> </span><span class="n" style="color: #333;">ptr</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">4</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3691" 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">
3691
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<td class="diff-line-num new_line old" data-linenumber="3695" 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="LC3691" class="line" lang="c"> <span class="idiff left right"> </span><span class="n" style="color: #333;">_exonbounds</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_loadu_si128</span><span class="p">((</span><span class="n" style="color: #333;">__m128i</span> <span class="o" style="font-weight: 600;">*</span><span class="p">)</span> <span class="n" style="color: #333;">ptr</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3692" 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">
3692
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<td class="diff-line-num new_line old" data-linenumber="3695" 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="LC3692" class="line" lang="c"> <span class="idiff left right"> </span><span class="n" style="color: #333;">_diff</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_cmpgt_epi32</span><span class="p">(</span><span class="n" style="color: #333;">_exonbounds</span><span class="p">,</span><span class="n" style="color: #333;">_trstart</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3693" 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">
3693
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<td class="diff-line-num new_line old" data-linenumber="3695" 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="LC3693" class="line" lang="c"> <span class="idiff left right"> </span><span class="p">}</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3694" 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">
3694
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<td class="diff-line-num new_line old" data-linenumber="3695" 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="LC3694" class="line" lang="c"> <span class="idiff left right"> </span><span class="n" style="color: #333;">matchbits</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_movemask_ps</span><span class="p">(</span><span class="n" style="color: #333;">_mm_castsi128_ps</span><span class="p">(</span><span class="n" style="color: #333;">_diff</span><span class="p">));</span></span>
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3695
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<td class="diff-line-num new_line old" data-linenumber="3695" 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="LC3695" class="line" lang="c"> <span class="idiff left right"> </span><span class="n" style="color: #333;">exoni</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">count_trailing_zeroes_32</span><span class="p">(</span><span class="n" style="color: #333;">matchbits</span><span class="p">);</span></span>
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3695
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<pre style="margin: 0;">+<span id="LC3695" class="line" lang="c"> <span class="n" style="color: #333;">_trstart</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_set1_epi32</span><span class="p">(</span><span class="n" style="color: #333;">trstart</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3696" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3696
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<pre style="margin: 0;">+<span id="LC3696" class="line" lang="c"> <span class="n" style="color: #333;">ptr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">exonbounds</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3697" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3697
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<pre style="margin: 0;">+<span id="LC3697" class="line" lang="c"> <span class="n" style="color: #333;">_exonbounds</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_loadu_si128</span><span class="p">((</span><span class="n" style="color: #333;">__m128i</span> <span class="o" style="font-weight: 600;">*</span><span class="p">)</span> <span class="n" style="color: #333;">ptr</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3698" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3698
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<pre style="margin: 0;">+<span id="LC3698" class="line" lang="c"> <span class="n" style="color: #333;">_diff</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_cmpgt_epi32</span><span class="p">(</span><span class="n" style="color: #333;">_exonbounds</span><span class="p">,</span><span class="n" style="color: #333;">_trstart</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3699" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3699
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<pre style="margin: 0;">+<span id="LC3699" class="line" lang="c"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">all_zero_p</span><span class="p">(</span><span class="n" style="color: #333;">_diff</span><span class="p">))</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3700" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3700
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<pre style="margin: 0;">+<span id="LC3700" class="line" lang="c"> <span class="idiff left right"> </span><span class="n" style="color: #333;">exoni</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">4</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3701" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3701
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<pre style="margin: 0;">+<span id="LC3701" class="line" lang="c"> <span class="idiff left right"> </span><span class="n" style="color: #333;">ptr</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">4</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3702" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3702
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<pre style="margin: 0;">+<span id="LC3702" class="line" lang="c"> <span class="idiff left right"> </span><span class="n" style="color: #333;">_exonbounds</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_loadu_si128</span><span class="p">((</span><span class="n" style="color: #333;">__m128i</span> <span class="o" style="font-weight: 600;">*</span><span class="p">)</span> <span class="n" style="color: #333;">ptr</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3703" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3703
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<pre style="margin: 0;">+<span id="LC3703" class="line" lang="c"> <span class="idiff left right"> </span><span class="n" style="color: #333;">_diff</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_cmpgt_epi32</span><span class="p">(</span><span class="n" style="color: #333;">_exonbounds</span><span class="p">,</span><span class="n" style="color: #333;">_trstart</span><span class="p">);</span></span>
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3704
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<pre style="margin: 0;">+<span id="LC3704" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3705" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3705
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<pre style="margin: 0;">+<span id="LC3705" class="line" lang="c"> <span class="n" style="color: #333;">matchbits</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_movemask_ps</span><span class="p">(</span><span class="n" style="color: #333;">_mm_castsi128_ps</span><span class="p">(</span><span class="n" style="color: #333;">_diff</span><span class="p">));</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3706" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3706
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<pre style="margin: 0;">+<span id="LC3706" class="line" lang="c"> <span class="n" style="color: #333;">exoni</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">count_trailing_zeroes_32</span><span class="p">(</span><span class="n" style="color: #333;">matchbits</span><span class="p">);</span></span>
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3696
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<td class="diff-line-num new_line" data-linenumber="3707" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3707
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<pre style="margin: 0;"> <span id="LC3707" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#else</span></span>
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3697
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<td class="diff-line-num new_line old" data-linenumber="3708" 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="LC3697" class="line" lang="c"> <span class="idiff left right"> </span><span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">exoni</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">nexons</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">exonbounds</span><span class="p">[</span><span class="n" style="color: #333;">exoni</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">trstart</span><span class="p">)</span> <span class="p">{</span></span>
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3698
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<td class="diff-line-num new_line old" data-linenumber="3708" 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="LC3698" class="line" lang="c"> <span class="idiff left right"> </span><span class="n" style="color: #333;">exoni</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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3699
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<td class="diff-line-num new_line old" data-linenumber="3708" 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="LC3699" class="line" lang="c"> <span class="idiff left right"> </span><span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3708" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3708
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<pre style="margin: 0;">+<span id="LC3708" class="line" lang="c"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">exoni</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">nexons</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">exonbounds</span><span class="p">[</span><span class="n" style="color: #333;">exoni</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">trstart</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3709" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3709
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<pre style="margin: 0;">+<span id="LC3709" class="line" lang="c"> <span class="idiff left right"> </span><span class="n" style="color: #333;">exoni</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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3710
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<pre style="margin: 0;">+<span id="LC3710" class="line" lang="c"> <span class="p">}</span></span>
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3700
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<td class="diff-line-num new_line" data-linenumber="3711" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3711
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<pre style="margin: 0;"> <span id="LC3711" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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3701
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<td class="diff-line-num new_line old" data-linenumber="3712" 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="LC3701" class="line" lang="c"></span>
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3702
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<td class="diff-line-num new_line old" data-linenumber="3712" 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="LC3702" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">exoni</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">nexons</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3703" 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">
3703
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<td class="diff-line-num new_line old" data-linenumber="3712" 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="LC3703" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"ABORTING BECAUSE OF EXONI %d >= NEXONS %d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">exoni</span><span class="p">,</span><span class="n" style="color: #333;">nexons</span><span class="p">));</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3712" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3712
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<pre style="margin: 0;">+<span id="LC3712" class="line" lang="c"> </span>
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<td class="diff-line-num new new_line" data-linenumber="3713" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3713
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<pre style="margin: 0;">+<span id="LC3713" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">exoni</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">nexons</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3714" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3714
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<pre style="margin: 0;">+<span id="LC3714" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"ABORTING BECAUSE OF EXONI %d >= NEXONS %d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">exoni</span><span class="p">,</span><span class="n" style="color: #333;">nexons</span><span class="p">));</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3715" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3715
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<pre style="margin: 0;">+<span id="LC3715" class="line" lang="c"> <span class="n" style="color: #333;">abortp</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3716" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3716
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<pre style="margin: 0;">+<span id="LC3716" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3717" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3717
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<pre style="margin: 0;">+<span id="LC3717" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"(9) exoni %d out of nexons %d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">exoni</span><span class="p">,</span><span class="n" style="color: #333;">nexons</span><span class="p">));</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3718" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3718
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<pre style="margin: 0;">+<span id="LC3718" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">exoni</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3719" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3719
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<pre style="margin: 0;">+<span id="LC3719" class="line" lang="c"> <span class="n" style="color: #333;">exonpos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">trstart</span><span class="p">;</span></span>
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3720
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<pre style="margin: 0;">+<span id="LC3720" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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3721
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<pre style="margin: 0;">+<span id="LC3721" class="line" lang="c"> <span class="n" style="color: #333;">exonpos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">trstart</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">exonbounds</span><span class="p">[</span><span class="n" style="color: #333;">exoni</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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3722
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<pre style="margin: 0;">+<span id="LC3722" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3723" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3723
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<pre style="margin: 0;">+<span id="LC3723" class="line" lang="c"> <span class="n" style="color: #333;">exon_residual</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">exonbounds</span><span class="p">[</span><span class="n" style="color: #333;">exoni</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">trstart</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3724" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3724
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<pre style="margin: 0;">+<span id="LC3724" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"exoni %d => exon_residual %d, exonpos %d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">exoni</span><span class="p">,</span><span class="n" style="color: #333;">exon_residual</span><span class="p">,</span><span class="n" style="color: #333;">exonpos</span><span class="p">));</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3725" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3725
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<pre style="margin: 0;">+<span id="LC3725" class="line" lang="c"> </span>
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<td class="diff-line-num new new_line" data-linenumber="3726" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3726
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<pre style="margin: 0;">+<span id="LC3726" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Generate one substring per exon */</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3727" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3727
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<pre style="margin: 0;">+<span id="LC3727" class="line" lang="c"> <span class="n" style="color: #333;">genomicpos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">exonstarts</span><span class="p">[</span><span class="n" style="color: #333;">exoni</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">exonpos</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/* gplus */</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3728" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3728
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<pre style="margin: 0;">+<span id="LC3728" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"genomicpos %u = %u + %u - 1</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">genomicpos</span><span class="p">,</span><span class="n" style="color: #333;">exonstarts</span><span class="p">[</span><span class="n" style="color: #333;">exoni</span><span class="p">],</span><span class="n" style="color: #333;">exonpos</span><span class="p">));</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3729" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3729
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<pre style="margin: 0;">+<span id="LC3729" class="line" lang="c"> <span class="n" style="color: #333;">align_residual</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">queryend</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">querystart</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3730" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3730
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<pre style="margin: 0;">+<span id="LC3730" class="line" lang="c"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">align_residual</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3731" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3731
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<pre style="margin: 0;">+<span id="LC3731" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"abortp %d, align_residual %d, exon_residual %d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">abortp</span><span class="p">,</span><span class="n" style="color: #333;">align_residual</span><span class="p">,</span><span class="n" style="color: #333;">exon_residual</span><span class="p">));</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3732" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3732
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<pre style="margin: 0;">+<span id="LC3732" class="line" lang="c"> <span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">align_residual</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">exon_residual</span><span class="p">)</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">align_residual</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">exon_residual</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3733" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3733
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<pre style="margin: 0;">+<span id="LC3733" class="line" lang="c"> <span class="n" style="color: #333;">queryend</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">querystart</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">len</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/* tplus */</span></span>
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3734
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<pre style="margin: 0;">+<span id="LC3734" class="line" lang="c"> </span>
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<td class="diff-line-num new new_line" data-linenumber="3735" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3735
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<pre style="margin: 0;">+<span id="LC3735" class="line" lang="c"> <span class="n" style="color: #333;">alignstart</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">chroffset</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">genomicpos</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3736" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3736
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<pre style="margin: 0;">+<span id="LC3736" class="line" lang="c"> <span class="n" style="color: #333;">alignend</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alignstart</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">len</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/* gplus */</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3737" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3737
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<pre style="margin: 0;">+<span id="LC3737" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">left</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alignstart</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">querystart</span><span class="p">);</span> <span class="cm" style="color: #998; font-style: italic;">/* tplus == gminus */</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3738" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3738
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<pre style="margin: 0;">+<span id="LC3738" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"tr ultrafast gap case 1 1st part query %d..%d, align %u..%u [%u..%u], left %u = %u - %d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span></span>
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3739
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<pre style="margin: 0;">+<span id="LC3739" class="line" lang="c"> <span class="n" style="color: #333;">querystart</span><span class="p">,</span><span class="n" style="color: #333;">queryend</span><span class="p">,</span><span class="n" style="color: #333;">alignstart</span><span class="p">,</span><span class="n" style="color: #333;">alignend</span><span class="p">,</span><span class="n" style="color: #333;">alignstart</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">chroffset</span><span class="p">,</span><span class="n" style="color: #333;">alignend</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">chroffset</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3740" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3740
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<pre style="margin: 0;">+<span id="LC3740" class="line" lang="c"> <span class="n" style="color: #333;">left</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">chroffset</span><span class="p">,</span><span class="n" style="color: #333;">alignstart</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">chroffset</span><span class="p">,</span><span class="n" style="color: #333;">querystart</span><span class="p">));</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3741" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3741
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<pre style="margin: 0;">+<span id="LC3741" class="line" lang="c"> </span>
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<td class="diff-line-num new new_line" data-linenumber="3742" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3742
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<pre style="margin: 0;">+<span id="LC3742" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* tplus: push alignstart first */</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3743" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3743
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<pre style="margin: 0;">+<span id="LC3743" class="line" lang="c"> <span class="n" style="color: #333;">endpoints</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Uintlist_push</span><span class="p">(</span><span class="n" style="color: #333;">endpoints</span><span class="p">,(</span><span class="n" style="color: #333;">Chrpos_T</span><span class="p">)</span> <span class="p">(</span><span class="n" style="color: #333;">alignstart</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">chroffset</span><span class="p">));</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3744" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3744
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<pre style="margin: 0;">+<span id="LC3744" class="line" lang="c"> <span class="n" style="color: #333;">endpoints</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Uintlist_push</span><span class="p">(</span><span class="n" style="color: #333;">endpoints</span><span class="p">,(</span><span class="n" style="color: #333;">Chrpos_T</span><span class="p">)</span> <span class="p">(</span><span class="n" style="color: #333;">alignend</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">chroffset</span><span class="p">));</span></span>
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3745
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<pre style="margin: 0;">+<span id="LC3745" class="line" lang="c"> </span>
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3746
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<pre style="margin: 0;">+<span id="LC3746" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">align_residual</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">exon_residual</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3747" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3747
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<pre style="margin: 0;">+<span id="LC3747" class="line" lang="c"> <span class="n" style="color: #333;">exon_residual</span> <span class="o" style="font-weight: 600;">-=</span> <span class="n" style="color: #333;">align_residual</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/* Need to know this if we have a following deletion */</span></span>
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3748
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<pre style="margin: 0;">+<span id="LC3748" class="line" lang="c"> <span class="n" style="color: #333;">align_residual</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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3749
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<pre style="margin: 0;">+<span id="LC3749" class="line" lang="c"> <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="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">exoni</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">nexons</span><span class="p">)</span> <span class="p">{</span></span>
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3750
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<pre style="margin: 0;">+<span id="LC3750" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Aligning past the end of the transcript */</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3751" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3751
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<pre style="margin: 0;">+<span id="LC3751" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"2 ABORTING BECAUSE ALIGNING PAST END OF TRANSCRIPT</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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3752
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<pre style="margin: 0;">+<span id="LC3752" class="line" lang="c"> <span class="n" style="color: #333;">align_residual</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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3704
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3753
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<pre style="margin: 0;"> <span id="LC3753" class="line" lang="c"> <span class="n" style="color: #333;">abortp</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="3705" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3705
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3754
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<pre style="margin: 0;"> <span id="LC3754" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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3706
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<td class="diff-line-num new_line old" data-linenumber="3755" 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="LC3706" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"(9) exoni %d out of nexons %d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">exoni</span><span class="p">,</span><span class="n" style="color: #333;">nexons</span><span class="p">));</span></span>
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3707
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<pre style="margin: 0;">-<span id="LC3707" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">exoni</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3708" 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">
3708
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<pre style="margin: 0;">-<span id="LC3708" class="line" lang="c"> <span class="n" style="color: #333;">exonpos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">trstart</span><span class="p">;</span></span>
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3709
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<td class="diff-line-num new_line old" data-linenumber="3755" 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="LC3709" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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3710
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<td class="diff-line-num new_line old" data-linenumber="3755" 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="LC3710" class="line" lang="c"> <span class="n" style="color: #333;">exonpos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">trstart</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">exonbounds</span><span class="p">[</span><span class="n" style="color: #333;">exoni</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 old old_line" data-linenumber="3711" 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">
3711
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<td class="diff-line-num new_line old" data-linenumber="3755" 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="LC3711" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3712" 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">
3712
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<td class="diff-line-num new_line old" data-linenumber="3755" 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="LC3712" class="line" lang="c"> <span class="n" style="color: #333;">exon_residual</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">exonbounds</span><span class="p">[</span><span class="n" style="color: #333;">exoni</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">trstart</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3713" 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">
3713
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<td class="diff-line-num new_line old" data-linenumber="3755" 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="LC3713" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"exoni %d => exon_residual %d, exonpos %d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">exoni</span><span class="p">,</span><span class="n" style="color: #333;">exon_residual</span><span class="p">,</span><span class="n" style="color: #333;">exonpos</span><span class="p">));</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3714" 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">
3714
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<td class="diff-line-num new_line old" data-linenumber="3755" 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="LC3714" class="line" lang="c"></span>
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<td class="diff-line-num old old_line" data-linenumber="3715" 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">
3715
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<td class="diff-line-num new_line old" data-linenumber="3755" 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="LC3715" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Generate one substring per exon */</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3716" 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">
3716
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<td class="diff-line-num new_line old" data-linenumber="3755" 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="LC3716" class="line" lang="c"> <span class="n" style="color: #333;">genomicpos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">exonstarts</span><span class="p">[</span><span class="n" style="color: #333;">exoni</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">exonpos</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/* gplus */</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3717" 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">
3717
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<td class="diff-line-num new_line old" data-linenumber="3755" 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="LC3717" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"genomicpos %u = %u + %u - 1</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">genomicpos</span><span class="p">,</span><span class="n" style="color: #333;">exonstarts</span><span class="p">[</span><span class="n" style="color: #333;">exoni</span><span class="p">],</span><span class="n" style="color: #333;">exonpos</span><span class="p">));</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3718" 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">
3718
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<td class="diff-line-num new_line old" data-linenumber="3755" 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="LC3718" class="line" lang="c"> <span class="n" style="color: #333;">align_residual</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">queryend</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">querystart</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3719" 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">
3719
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<td class="diff-line-num new_line old" data-linenumber="3755" 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="LC3719" class="line" lang="c"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">align_residual</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3720" 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">
3720
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<td class="diff-line-num new_line old" data-linenumber="3755" 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="LC3720" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"abortp %d, align_residual %d, exon_residual %d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">abortp</span><span class="p">,</span><span class="n" style="color: #333;">align_residual</span><span class="p">,</span><span class="n" style="color: #333;">exon_residual</span><span class="p">));</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3721" 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">
3721
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<td class="diff-line-num new_line old" data-linenumber="3755" 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="LC3721" class="line" lang="c"> <span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">align_residual</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">exon_residual</span><span class="p">)</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">align_residual</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">exon_residual</span><span class="p">;</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="3722" 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">
3722
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<td class="diff-line-num new_line old" data-linenumber="3755" 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="LC3722" class="line" lang="c"> <span class="n" style="color: #333;">queryend</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">querystart</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">len</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/* tplus */</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="3723" 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">
3723
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<td class="diff-line-num new_line old" data-linenumber="3755" 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="LC3723" class="line" lang="c"> </span>
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<td class="diff-line-num old old_line" data-linenumber="3724" 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">
3724
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<td class="diff-line-num new_line old" data-linenumber="3755" 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="LC3724" class="line" lang="c"> <span class="n" style="color: #333;">alignstart</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">chroffset</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">genomicpos</span><span class="p">;</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="3725" 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">
3725
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<td class="diff-line-num new_line old" data-linenumber="3755" 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="LC3725" class="line" lang="c"> <span class="n" style="color: #333;">alignend</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alignstart</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">len</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/* gplus */</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3726" 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">
3726
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<td class="diff-line-num new_line old" data-linenumber="3755" 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="LC3726" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">left</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alignstart</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">querystart</span><span class="p">);</span> <span class="cm" style="color: #998; font-style: italic;">/* tplus == gminus */</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3727" 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">
3727
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<td class="diff-line-num new_line old" data-linenumber="3755" 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="LC3727" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"tr ultrafast gap case 1 1st part query %d..%d, align %u..%u [%u..%u], left %u = %u - %d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3728" 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">
3728
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<pre style="margin: 0;">-<span id="LC3728" class="line" lang="c"> <span class="n" style="color: #333;">querystart</span><span class="p">,</span><span class="n" style="color: #333;">queryend</span><span class="p">,</span><span class="n" style="color: #333;">alignstart</span><span class="p">,</span><span class="n" style="color: #333;">alignend</span><span class="p">,</span><span class="n" style="color: #333;">alignstart</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">chroffset</span><span class="p">,</span><span class="n" style="color: #333;">alignend</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">chroffset</span><span class="p">,</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3729" 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">
3729
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<td class="diff-line-num new_line old" data-linenumber="3755" 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="LC3729" class="line" lang="c"> <span class="n" style="color: #333;">left</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">chroffset</span><span class="p">,</span><span class="n" style="color: #333;">alignstart</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">chroffset</span><span class="p">,</span><span class="n" style="color: #333;">querystart</span><span class="p">));</span></span>
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3730
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<td class="diff-line-num new_line old" data-linenumber="3755" 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="LC3730" class="line" lang="c"> </span>
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<td class="diff-line-num old old_line" data-linenumber="3731" 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">
3731
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<td class="diff-line-num new_line old" data-linenumber="3755" 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="LC3731" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* tplus: push alignstart first */</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3732" 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">
3732
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<td class="diff-line-num new_line old" data-linenumber="3755" 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="LC3732" class="line" lang="c"> <span class="n" style="color: #333;">endpoints</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Uintlist_push</span><span class="p">(</span><span class="n" style="color: #333;">endpoints</span><span class="p">,(</span><span class="n" style="color: #333;">Chrpos_T</span><span class="p">)</span> <span class="p">(</span><span class="n" style="color: #333;">alignstart</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">chroffset</span><span class="p">));</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3733" 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">
3733
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<td class="diff-line-num new_line old" data-linenumber="3755" 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="LC3733" class="line" lang="c"> <span class="n" style="color: #333;">endpoints</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Uintlist_push</span><span class="p">(</span><span class="n" style="color: #333;">endpoints</span><span class="p">,(</span><span class="n" style="color: #333;">Chrpos_T</span><span class="p">)</span> <span class="p">(</span><span class="n" style="color: #333;">alignend</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">chroffset</span><span class="p">));</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3734" 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">
3734
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<pre style="margin: 0;">-<span id="LC3734" class="line" lang="c"></span>
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<td class="diff-line-num old old_line" data-linenumber="3735" 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">
3735
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<td class="diff-line-num new_line old" data-linenumber="3755" 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="LC3735" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">align_residual</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">exon_residual</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3736" 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">
3736
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<td class="diff-line-num new_line old" data-linenumber="3755" 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="LC3736" class="line" lang="c"> <span class="n" style="color: #333;">exon_residual</span> <span class="o" style="font-weight: 600;">-=</span> <span class="n" style="color: #333;">align_residual</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/* Need to know this if we have a following deletion */</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3737" 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">
3737
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<pre style="margin: 0;">-<span id="LC3737" class="line" lang="c"> <span class="n" style="color: #333;">align_residual</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3738" 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">
3738
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<pre style="margin: 0;">-<span id="LC3738" class="line" lang="c"> <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="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">exoni</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">nexons</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3739" 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">
3739
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<td class="diff-line-num new_line old" data-linenumber="3755" 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="LC3739" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Aligning past the end of the transcript */</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3740" 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">
3740
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<pre style="margin: 0;">-<span id="LC3740" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"2 ABORTING BECAUSE ALIGNING PAST END OF TRANSCRIPT</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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3741
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<pre style="margin: 0;">-<span id="LC3741" class="line" lang="c"> <span class="n" style="color: #333;">align_residual</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3742" 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">
3742
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<td class="diff-line-num new_line old" data-linenumber="3755" 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="LC3742" class="line" lang="c"> <span class="n" style="color: #333;">abortp</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3743" 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">
3743
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<td class="diff-line-num new_line old" data-linenumber="3755" 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="LC3743" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3744" 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">
3744
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<pre style="margin: 0;">-<span id="LC3744" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* nintrons += 1; */</span></span>
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3745
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<pre style="margin: 0;">-<span id="LC3745" class="line" lang="c"> <span class="n" style="color: #333;">align_residual</span> <span class="o" style="font-weight: 600;">-=</span> <span class="n" style="color: #333;">len</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3746" 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">
3746
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<td class="diff-line-num new_line old" data-linenumber="3755" 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="LC3746" class="line" lang="c"> <span class="n" style="color: #333;">querystart</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">len</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/* tplus */</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3747" 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">
3747
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<pre style="margin: 0;">-<span id="LC3747" class="line" lang="c"> <span class="n" style="color: #333;">genomicpos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">exonstarts</span><span class="p">[</span><span class="n" style="color: #333;">exoni</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="cm" style="color: #998; font-style: italic;">/* gplus */</span></span>
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3748
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<pre style="margin: 0;">-<span id="LC3748" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"genomicpos %u = %u - 1</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">genomicpos</span><span class="p">,</span><span class="n" style="color: #333;">exonstarts</span><span class="p">[</span><span class="n" style="color: #333;">exoni</span><span class="p">]));</span></span>
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3749
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<pre style="margin: 0;">-<span id="LC3749" class="line" lang="c"> <span class="n" style="color: #333;">exon_residual</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">exonbounds</span><span class="p">[</span><span class="n" style="color: #333;">exoni</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">exonbounds</span><span class="p">[</span><span class="n" style="color: #333;">exoni</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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3750
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<pre style="margin: 0;">-<span id="LC3750" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"INTRON</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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3751
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<td class="diff-line-num new_line old" data-linenumber="3755" 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="LC3751" class="line" lang="c"> <span class="n" style="color: #333;">gaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Intlist_push</span><span class="p">(</span><span class="n" style="color: #333;">gaps</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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3752
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<pre style="margin: 0;">-<span id="LC3752" class="line" lang="c"> <span class="p">}</span></span>
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3753
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<pre style="margin: 0;">-<span id="LC3753" class="line" lang="c"> <span class="p">}</span></span>
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3755
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<pre style="margin: 0;">+<span id="LC3755" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* nintrons += 1; */</span></span>
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3756
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<pre style="margin: 0;">+<span id="LC3756" class="line" lang="c"> <span class="n" style="color: #333;">align_residual</span> <span class="o" style="font-weight: 600;">-=</span> <span class="n" style="color: #333;">len</span><span class="p">;</span></span>
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3757
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<pre style="margin: 0;">+<span id="LC3757" class="line" lang="c"> <span class="n" style="color: #333;">querystart</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">len</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/* tplus */</span></span>
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3758
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<pre style="margin: 0;">+<span id="LC3758" class="line" lang="c"> <span class="n" style="color: #333;">genomicpos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">exonstarts</span><span class="p">[</span><span class="n" style="color: #333;">exoni</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="cm" style="color: #998; font-style: italic;">/* gplus */</span></span>
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3759
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<pre style="margin: 0;">+<span id="LC3759" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"genomicpos %u = %u - 1</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">genomicpos</span><span class="p">,</span><span class="n" style="color: #333;">exonstarts</span><span class="p">[</span><span class="n" style="color: #333;">exoni</span><span class="p">]));</span></span>
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3760
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<pre style="margin: 0;">+<span id="LC3760" class="line" lang="c"> <span class="n" style="color: #333;">exon_residual</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">exonbounds</span><span class="p">[</span><span class="n" style="color: #333;">exoni</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">exonbounds</span><span class="p">[</span><span class="n" style="color: #333;">exoni</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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3761
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<pre style="margin: 0;">+<span id="LC3761" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"INTRON</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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3762
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<pre style="margin: 0;">+<span id="LC3762" class="line" lang="c"> <span class="n" style="color: #333;">gaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Intlist_push</span><span class="p">(</span><span class="n" style="color: #333;">gaps</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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3754
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3763
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<pre style="margin: 0;"> <span id="LC3763" class="line" lang="c"> <span class="p">}</span></span>
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3764
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<pre style="margin: 0;">+<span id="LC3764" class="line" lang="c"> <span class="p">}</span></span>
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3765
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<pre style="margin: 0;">+<span id="LC3765" class="line" lang="c"> <span class="p">}</span></span>
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3766
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<pre style="margin: 0;">+<span id="LC3766" class="line" lang="c"> </span>
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3767
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<pre style="margin: 0;">+<span id="LC3767" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* gap */</span></span>
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3768
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<pre style="margin: 0;">+<span id="LC3768" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"INDEL: last piece %d | nindels %d | next piece %d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">len</span><span class="p">,</span><span class="n" style="color: #333;">nindels</span><span class="p">,</span><span class="n" style="color: #333;">exon_residual</span><span class="p">));</span></span>
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3769
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<pre style="margin: 0;">+<span id="LC3769" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"exon residual %d vs nindels %d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">exon_residual</span><span class="p">,</span><span class="n" style="color: #333;">nindels</span><span class="p">));</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3770" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3770
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<pre style="margin: 0;">+<span id="LC3770" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">abortp</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3771" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3771
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<pre style="margin: 0;">+<span id="LC3771" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Skip */</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3772" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3772
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<pre style="margin: 0;">+<span id="LC3772" class="line" lang="c"> <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="cm" style="color: #998; font-style: italic;">/*len <= nindels ||*/</span><span class="n" style="color: #333;">exon_residual</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">nindels</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3773" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3773
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<pre style="margin: 0;">+<span id="LC3773" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"ABORTING BECAUSE INDEL OVERLAPS SPLICE SITE (5)</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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3774
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<pre style="margin: 0;">+<span id="LC3774" class="line" lang="c"> <span class="n" style="color: #333;">abortp</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3775" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3775
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<pre style="margin: 0;">+<span id="LC3775" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3776" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3776
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<pre style="margin: 0;">+<span id="LC3776" class="line" lang="c"> <span class="n" style="color: #333;">gaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Intlist_push</span><span class="p">(</span><span class="n" style="color: #333;">gaps</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;">adj</span><span class="p">);</span></span>
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3777
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<pre style="margin: 0;">+<span id="LC3777" class="line" lang="c"> <span class="p">}</span></span>
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3778
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<pre style="margin: 0;">+<span id="LC3778" class="line" lang="c"> </span>
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<td class="diff-line-num new new_line" data-linenumber="3779" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3779
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<pre style="margin: 0;">+<span id="LC3779" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* second part */</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3780" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3780
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<pre style="margin: 0;">+<span id="LC3780" class="line" lang="c"> <span class="n" style="color: #333;">tr_left</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tr_left1</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3781" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3781
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<pre style="margin: 0;">+<span id="LC3781" class="line" lang="c"> <span class="n" style="color: #333;">querystart</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">indel_pos</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">ninserts</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3782" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3782
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<pre style="margin: 0;">+<span id="LC3782" class="line" lang="c"> <span class="n" style="color: #333;">queryend</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">querylength</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3783" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3783
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<pre style="margin: 0;">+<span id="LC3783" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</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;">Analyzing query %d..%d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">querystart</span><span class="p">,</span><span class="n" style="color: #333;">queryend</span><span class="p">));</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3784" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3784
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<pre style="margin: 0;">+<span id="LC3784" class="line" lang="c"> </span>
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3785
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<pre style="margin: 0;">+<span id="LC3785" class="line" lang="c"> <span class="n" style="color: #333;">trstart</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">transcript_diag1</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">querystart</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/* tplus */</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3786" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3786
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<pre style="margin: 0;">+<span id="LC3786" class="line" lang="c"> <span class="n" style="color: #333;">overall_trend</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">transcript_diag1</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">queryend</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/* tplus */</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3787" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3787
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<pre style="margin: 0;">+<span id="LC3787" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"transcript_diag %d, trstart %d, trend %d, tr_left %u</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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3788
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<pre style="margin: 0;">+<span id="LC3788" class="line" lang="c"> <span class="n" style="color: #333;">transcript_diag1</span><span class="p">,</span><span class="n" style="color: #333;">trstart</span><span class="p">,</span><span class="n" style="color: #333;">overall_trend</span><span class="p">,</span><span class="n" style="color: #333;">tr_left</span><span class="p">));</span></span>
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3789
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<pre style="margin: 0;">+<span id="LC3789" class="line" lang="c"> </span>
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<td class="diff-line-num new new_line" data-linenumber="3790" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3790
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<pre style="margin: 0;">+<span id="LC3790" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"Searching for exoni for trstart %d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">trstart</span><span class="p">));</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3791" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3791
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<pre style="margin: 0;">+<span id="LC3791" class="line" lang="c"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">exoni</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">nexons</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">exonbounds</span><span class="p">[</span><span class="n" style="color: #333;">exoni</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">trstart</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3792" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3792
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<pre style="margin: 0;">+<span id="LC3792" class="line" lang="c"> <span class="n" style="color: #333;">exoni</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3793" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3793
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<pre style="margin: 0;">+<span id="LC3793" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3794" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3794
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<pre style="margin: 0;">+<span id="LC3794" class="line" lang="c"> </span>
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<td class="diff-line-num new new_line" data-linenumber="3795" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3795
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<pre style="margin: 0;">+<span id="LC3795" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">exoni</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">nexons</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3796" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3796
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<pre style="margin: 0;">+<span id="LC3796" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"ABORTING BECAUSE OF EXONI %d >= NEXONS %d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">exoni</span><span class="p">,</span><span class="n" style="color: #333;">nexons</span><span class="p">));</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="3797" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3797
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<pre style="margin: 0;">+<span id="LC3797" class="line" lang="c"> <span class="n" style="color: #333;">abortp</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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<td class="diff-line-num new old_line" data-linenumber="3755" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="3798" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3798
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<pre style="margin: 0;">+<span id="LC3798" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3799" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3799
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<pre style="margin: 0;">+<span id="LC3799" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"(10) exoni %d out of nexons %d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">exoni</span><span class="p">,</span><span class="n" style="color: #333;">nexons</span><span class="p">));</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3800" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3800
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<pre style="margin: 0;">+<span id="LC3800" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">exoni</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>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="3755" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="3801" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3801
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<pre style="margin: 0;">+<span id="LC3801" class="line" lang="c"> <span class="n" style="color: #333;">exonpos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">trstart</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3802" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3802
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<pre style="margin: 0;">+<span id="LC3802" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3803" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3803
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<pre style="margin: 0;">+<span id="LC3803" class="line" lang="c"> <span class="n" style="color: #333;">exonpos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">trstart</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">exonbounds</span><span class="p">[</span><span class="n" style="color: #333;">exoni</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">];</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3804" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3804
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<pre style="margin: 0;">+<span id="LC3804" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num new old_line" data-linenumber="3755" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="3805" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3805
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<pre style="margin: 0;">+<span id="LC3805" class="line" lang="c"> <span class="n" style="color: #333;">exon_residual</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">exonbounds</span><span class="p">[</span><span class="n" style="color: #333;">exoni</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">trstart</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3806" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3806
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<pre style="margin: 0;">+<span id="LC3806" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"exoni %d => exon_residual %d, exonpos %d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">exoni</span><span class="p">,</span><span class="n" style="color: #333;">exon_residual</span><span class="p">,</span><span class="n" style="color: #333;">exonpos</span><span class="p">));</span></span>
</pre>
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3755
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<td class="diff-line-num new_line" data-linenumber="3807" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3807
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<pre style="margin: 0;"> <span id="LC3807" class="line" lang="c"> </span>
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<td class="diff-line-num old old_line" data-linenumber="3756" 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">
3756
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<td class="diff-line-num new_line old" data-linenumber="3808" 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="LC3756" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* gap */</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3757" 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">
3757
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<td class="diff-line-num new_line old" data-linenumber="3808" 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="LC3757" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"INDEL: last piece %d | nindels %d | next piece %d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">len</span><span class="p">,</span><span class="n" style="color: #333;">nindels</span><span class="p">,</span><span class="n" style="color: #333;">exon_residual</span><span class="p">));</span></span>
</pre>
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3758
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<pre style="margin: 0;">-<span id="LC3758" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"exon residual %d vs nindels %d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">exon_residual</span><span class="p">,</span><span class="n" style="color: #333;">nindels</span><span class="p">));</span></span>
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3759
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<td class="diff-line-num new_line old" data-linenumber="3808" 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="LC3759" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">abortp</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3760" 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">
3760
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<td class="diff-line-num new_line old" data-linenumber="3808" 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="LC3760" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Skip */</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3761" 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">
3761
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<td class="diff-line-num new_line old" data-linenumber="3808" 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="LC3761" class="line" lang="c"> <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="cm" style="color: #998; font-style: italic;">/*len <= nindels ||*/</span><span class="n" style="color: #333;">exon_residual</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">nindels</span><span class="p">)</span> <span class="p">{</span></span>
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3762
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<td class="diff-line-num new_line old" data-linenumber="3808" 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="LC3762" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"ABORTING BECAUSE INDEL OVERLAPS SPLICE SITE</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">));</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3808" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3808
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<pre style="margin: 0;">+<span id="LC3808" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Generate one substring per exon */</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3809" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3809
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<pre style="margin: 0;">+<span id="LC3809" class="line" lang="c"> <span class="n" style="color: #333;">genomicpos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">exonstarts</span><span class="p">[</span><span class="n" style="color: #333;">exoni</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">exonpos</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/* gplus */</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3810" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3810
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<pre style="margin: 0;">+<span id="LC3810" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"genomicpos %u = %u + %u - 1</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">genomicpos</span><span class="p">,</span><span class="n" style="color: #333;">exonstarts</span><span class="p">[</span><span class="n" style="color: #333;">exoni</span><span class="p">],</span><span class="n" style="color: #333;">exonpos</span><span class="p">));</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3811" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3811
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<pre style="margin: 0;">+<span id="LC3811" class="line" lang="c"> <span class="n" style="color: #333;">align_residual</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">queryend</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">querystart</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3812" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3812
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<pre style="margin: 0;">+<span id="LC3812" class="line" lang="c"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">align_residual</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3813" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3813
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<pre style="margin: 0;">+<span id="LC3813" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"abortp %d, align_residual %d, exon_residual %d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">abortp</span><span class="p">,</span><span class="n" style="color: #333;">align_residual</span><span class="p">,</span><span class="n" style="color: #333;">exon_residual</span><span class="p">));</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3814" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3814
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<pre style="margin: 0;">+<span id="LC3814" class="line" lang="c"> <span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">align_residual</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">exon_residual</span><span class="p">)</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">align_residual</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">exon_residual</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3815" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3815
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<pre style="margin: 0;">+<span id="LC3815" class="line" lang="c"> <span class="n" style="color: #333;">queryend</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">querystart</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">len</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/* tplus */</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3816" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3816
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<pre style="margin: 0;">+<span id="LC3816" class="line" lang="c"> </span>
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<td class="diff-line-num new new_line" data-linenumber="3817" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3817
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<pre style="margin: 0;">+<span id="LC3817" class="line" lang="c"> <span class="n" style="color: #333;">alignstart</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">chroffset</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">genomicpos</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3818" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3818
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<pre style="margin: 0;">+<span id="LC3818" class="line" lang="c"> <span class="n" style="color: #333;">alignend</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alignstart</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">len</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/* gplus */</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3819" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3819
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<pre style="margin: 0;">+<span id="LC3819" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">left</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alignstart</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">querystart</span><span class="p">);</span> <span class="cm" style="color: #998; font-style: italic;">/* tplus == gminus */</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3820" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3820
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<pre style="margin: 0;">+<span id="LC3820" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"tr ultrafast gap case 1 2nd part query %d..%d, align %u..%u [%u..%u], left %u = %u - %d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span></span>
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3821
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<pre style="margin: 0;">+<span id="LC3821" class="line" lang="c"> <span class="n" style="color: #333;">querystart</span><span class="p">,</span><span class="n" style="color: #333;">queryend</span><span class="p">,</span><span class="n" style="color: #333;">alignstart</span><span class="p">,</span><span class="n" style="color: #333;">alignend</span><span class="p">,</span><span class="n" style="color: #333;">alignstart</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">chroffset</span><span class="p">,</span><span class="n" style="color: #333;">alignend</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">chroffset</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3822" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3822
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<pre style="margin: 0;">+<span id="LC3822" class="line" lang="c"> <span class="n" style="color: #333;">left</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">chroffset</span><span class="p">,</span><span class="n" style="color: #333;">alignstart</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">chroffset</span><span class="p">,</span><span class="n" style="color: #333;">querystart</span><span class="p">));</span></span>
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3823
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<pre style="margin: 0;">+<span id="LC3823" class="line" lang="c"> </span>
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<td class="diff-line-num new new_line" data-linenumber="3824" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3824
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<pre style="margin: 0;">+<span id="LC3824" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* tplus: push alignstart first */</span></span>
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3825
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<pre style="margin: 0;">+<span id="LC3825" class="line" lang="c"> <span class="n" style="color: #333;">endpoints</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Uintlist_push</span><span class="p">(</span><span class="n" style="color: #333;">endpoints</span><span class="p">,(</span><span class="n" style="color: #333;">Chrpos_T</span><span class="p">)</span> <span class="p">(</span><span class="n" style="color: #333;">alignstart</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">chroffset</span><span class="p">));</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3826" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3826
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<pre style="margin: 0;">+<span id="LC3826" class="line" lang="c"> <span class="n" style="color: #333;">endpoints</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Uintlist_push</span><span class="p">(</span><span class="n" style="color: #333;">endpoints</span><span class="p">,(</span><span class="n" style="color: #333;">Chrpos_T</span><span class="p">)</span> <span class="p">(</span><span class="n" style="color: #333;">alignend</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">chroffset</span><span class="p">));</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3827" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3827
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<pre style="margin: 0;">+<span id="LC3827" class="line" lang="c"> </span>
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<td class="diff-line-num new new_line" data-linenumber="3828" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3828
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<pre style="margin: 0;">+<span id="LC3828" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">align_residual</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">exon_residual</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3829" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3829
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<pre style="margin: 0;">+<span id="LC3829" class="line" lang="c"> <span class="n" style="color: #333;">exon_residual</span> <span class="o" style="font-weight: 600;">-=</span> <span class="n" style="color: #333;">align_residual</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/* Need to know this if we have a following deletion */</span></span>
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3830
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<pre style="margin: 0;">+<span id="LC3830" class="line" lang="c"> <span class="n" style="color: #333;">align_residual</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3831" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3831
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<pre style="margin: 0;">+<span id="LC3831" class="line" lang="c"> <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="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">exoni</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">nexons</span><span class="p">)</span> <span class="p">{</span></span>
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3832
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<pre style="margin: 0;">+<span id="LC3832" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Aligning past the end of the transcript */</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3833" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3833
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<pre style="margin: 0;">+<span id="LC3833" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"2 ABORTING BECAUSE ALIGNING PAST END OF TRANSCRIPT</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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3834
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<pre style="margin: 0;">+<span id="LC3834" class="line" lang="c"> <span class="n" style="color: #333;">align_residual</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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3763
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3835
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<pre style="margin: 0;"> <span id="LC3835" class="line" lang="c"> <span class="n" style="color: #333;">abortp</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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3764
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<td class="diff-line-num new_line" data-linenumber="3836" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3836
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<pre style="margin: 0;"> <span id="LC3836" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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3765
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<pre style="margin: 0;">-<span id="LC3765" class="line" lang="c"> <span class="n" style="color: #333;">gaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Intlist_push</span><span class="p">(</span><span class="n" style="color: #333;">gaps</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;">adj</span><span class="p">);</span></span>
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3766
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<pre style="margin: 0;">-<span id="LC3766" class="line" lang="c"> <span class="p">}</span></span>
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3767
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<td class="diff-line-num new_line old" data-linenumber="3837" 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="LC3767" class="line" lang="c"></span>
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3768
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<td class="diff-line-num new_line old" data-linenumber="3837" 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="LC3768" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* second part */</span></span>
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3769
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<pre style="margin: 0;">-<span id="LC3769" class="line" lang="c"> <span class="n" style="color: #333;">tr_left</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tr_left1</span><span class="p">;</span></span>
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3770
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<pre style="margin: 0;">-<span id="LC3770" class="line" lang="c"> <span class="n" style="color: #333;">querystart</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">indel_pos</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">ninserts</span><span class="p">;</span></span>
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3771
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<td class="diff-line-num new_line old" data-linenumber="3837" 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="LC3771" class="line" lang="c"> <span class="n" style="color: #333;">queryend</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">querylength</span><span class="p">;</span></span>
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3772
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<td class="diff-line-num new_line old" data-linenumber="3837" 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="LC3772" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</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;">Analyzing query %d..%d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">querystart</span><span class="p">,</span><span class="n" style="color: #333;">queryend</span><span class="p">));</span></span>
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3773
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<td class="diff-line-num new_line old" data-linenumber="3837" 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="LC3773" class="line" lang="c"></span>
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3774
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<td class="diff-line-num new_line old" data-linenumber="3837" 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="LC3774" class="line" lang="c"> <span class="n" style="color: #333;">trstart</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">transcript_diag1</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">querystart</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/* tplus */</span></span>
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3775
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<td class="diff-line-num new_line old" data-linenumber="3837" 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="LC3775" class="line" lang="c"> <span class="n" style="color: #333;">overall_trend</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">transcript_diag1</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">queryend</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/* tplus */</span></span>
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3776
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<td class="diff-line-num new_line old" data-linenumber="3837" 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="LC3776" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"transcript_diag %d, trstart %d, trend %d, tr_left %u</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3777" 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">
3777
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<td class="diff-line-num new_line old" data-linenumber="3837" 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="LC3777" class="line" lang="c"> <span class="n" style="color: #333;">transcript_diag1</span><span class="p">,</span><span class="n" style="color: #333;">trstart</span><span class="p">,</span><span class="n" style="color: #333;">overall_trend</span><span class="p">,</span><span class="n" style="color: #333;">tr_left</span><span class="p">));</span></span>
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3778
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<td class="diff-line-num new_line old" data-linenumber="3837" 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="LC3778" class="line" lang="c"></span>
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3779
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<td class="diff-line-num new_line old" data-linenumber="3837" 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="LC3779" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"Searching for exoni for trstart %d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">trstart</span><span class="p">));</span></span>
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3780
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<td class="diff-line-num new_line old" data-linenumber="3837" 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="LC3780" class="line" lang="c"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">exoni</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">nexons</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">exonbounds</span><span class="p">[</span><span class="n" style="color: #333;">exoni</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">trstart</span><span class="p">)</span> <span class="p">{</span></span>
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3781
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<td class="diff-line-num new_line old" data-linenumber="3837" 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="LC3781" class="line" lang="c"> <span class="n" style="color: #333;">exoni</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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3837
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<pre style="margin: 0;">+<span id="LC3837" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* nintrons += 1; */</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3838" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3838
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<pre style="margin: 0;">+<span id="LC3838" class="line" lang="c"> <span class="n" style="color: #333;">align_residual</span> <span class="o" style="font-weight: 600;">-=</span> <span class="n" style="color: #333;">len</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3839" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3839
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<pre style="margin: 0;">+<span id="LC3839" class="line" lang="c"> <span class="n" style="color: #333;">querystart</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">len</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/* tplus */</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3840" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3840
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<pre style="margin: 0;">+<span id="LC3840" class="line" lang="c"> <span class="n" style="color: #333;">genomicpos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">exonstarts</span><span class="p">[</span><span class="n" style="color: #333;">exoni</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="cm" style="color: #998; font-style: italic;">/* gplus */</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3841" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3841
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<pre style="margin: 0;">+<span id="LC3841" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"genomicpos %u = %u - 1</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">genomicpos</span><span class="p">,</span><span class="n" style="color: #333;">exonstarts</span><span class="p">[</span><span class="n" style="color: #333;">exoni</span><span class="p">]));</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3842" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3842
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<pre style="margin: 0;">+<span id="LC3842" class="line" lang="c"> <span class="n" style="color: #333;">exon_residual</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">exonbounds</span><span class="p">[</span><span class="n" style="color: #333;">exoni</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">exonbounds</span><span class="p">[</span><span class="n" style="color: #333;">exoni</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">];</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3843" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3843
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<pre style="margin: 0;">+<span id="LC3843" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"INTRON</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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3844
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<pre style="margin: 0;">+<span id="LC3844" class="line" lang="c"> <span class="n" style="color: #333;">gaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Intlist_push</span><span class="p">(</span><span class="n" style="color: #333;">gaps</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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3782
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3845
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<pre style="margin: 0;"> <span id="LC3845" class="line" lang="c"> <span class="p">}</span></span>
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3846
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<pre style="margin: 0;">+<span id="LC3846" class="line" lang="c"> <span class="p">}</span></span>
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3847
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<pre style="margin: 0;">+<span id="LC3847" class="line" lang="c"> <span class="p">}</span></span>
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3848
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<pre style="margin: 0;">+<span id="LC3848" class="line" lang="c"> </span>
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<td class="diff-line-num new new_line" data-linenumber="3849" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3849
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<pre style="margin: 0;">+<span id="LC3849" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">abortp</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3850" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3850
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<pre style="margin: 0;">+<span id="LC3850" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"ABORTING PATH</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">));</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3851" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3851
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<pre style="margin: 0;">+<span id="LC3851" class="line" lang="c"> <span class="n" style="color: #333;">Uintlist_free</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">endpoints</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3852" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3852
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<pre style="margin: 0;">+<span id="LC3852" class="line" lang="c"> <span class="n" style="color: #333;">Intlist_free</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">gaps</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3853" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3853
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<pre style="margin: 0;">+<span id="LC3853" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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3854
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<pre style="margin: 0;">+<span id="LC3854" class="line" lang="c"> <span class="n" style="color: #333;">endpoints</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Uintlist_reverse</span><span class="p">(</span><span class="n" style="color: #333;">endpoints</span><span class="p">);</span> <span class="cm" style="color: #998; font-style: italic;">/* gplus */</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3855" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3855
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<pre style="margin: 0;">+<span id="LC3855" class="line" lang="c"> <span class="n" style="color: #333;">gaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Intlist_reverse</span><span class="p">(</span><span class="n" style="color: #333;">gaps</span><span class="p">);</span> <span class="cm" style="color: #998; font-style: italic;">/* gplus */</span></span>
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3856
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<pre style="margin: 0;">+<span id="LC3856" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"PLUS PATH %d. ENDPOINTS: %s. GAPS: %s</span><span class="se" style="color: #d14;">\n\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3857" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3857
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<pre style="margin: 0;">+<span id="LC3857" class="line" lang="c"> <span class="n" style="color: #333;">ngplus</span><span class="p">,</span><span class="n" style="color: #333;">Uintlist_to_string</span><span class="p">(</span><span class="n" style="color: #333;">endpoints</span><span class="p">),</span><span class="n" style="color: #333;">Intlist_to_string</span><span class="p">(</span><span class="n" style="color: #333;">gaps</span><span class="p">)));</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3858" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3858
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<pre style="margin: 0;">+<span id="LC3858" class="line" lang="c"> <span class="n" style="color: #333;">gplus_paths</span><span class="p">[</span><span class="n" style="color: #333;">ngplus</span><span class="o" style="font-weight: 600;">++</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Path_new</span><span class="p">(</span><span class="n" style="color: #333;">total_nmatches</span><span class="p">,</span><span class="n" style="color: #333;">trnum</span><span class="p">,</span><span class="n" style="color: #333;">overall_trstart</span><span class="p">,</span><span class="n" style="color: #333;">overall_trend</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3859" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3859
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<pre style="margin: 0;">+<span id="LC3859" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/*trim_low*/</span><span class="n" style="color: #333;">trim5</span><span class="p">,</span><span class="cm" style="color: #998; font-style: italic;">/*trim_high*/</span><span class="n" style="color: #333;">trim3</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3860" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3860
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<pre style="margin: 0;">+<span id="LC3860" class="line" lang="c"> <span class="n" style="color: #333;">chrnum</span><span class="p">,</span><span class="n" style="color: #333;">chroffset</span><span class="p">,</span><span class="n" style="color: #333;">chrhigh</span><span class="p">,</span><span class="n" style="color: #333;">chrlength</span><span class="p">,</span><span class="n" style="color: #333;">endpoints</span><span class="p">,</span><span class="n" style="color: #333;">gaps</span><span class="p">,</span><span class="n" style="color: #333;">concordantp</span><span class="p">);</span></span>
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3861
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<pre style="margin: 0;">+<span id="LC3861" class="line" lang="c"> <span class="p">}</span></span>
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3862
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<pre style="margin: 0;">+<span id="LC3862" class="line" lang="c"> </span>
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<td class="diff-line-num new new_line" data-linenumber="3863" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3863
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<pre style="margin: 0;">+<span id="LC3863" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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3864
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<pre style="margin: 0;">+<span id="LC3864" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Case 2 ultrafast gap: tplus, gminus. transcript_plusp == true && transcript_genestrand < 0 */</span></span>
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3865
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<pre style="margin: 0;">+<span id="LC3865" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"Case 2 ultrafast gap: tplus, gminus</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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3866
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<pre style="margin: 0;">+<span id="LC3866" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* sensedir = SENSE_FORWARD; */</span></span>
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3867
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<pre style="margin: 0;">+<span id="LC3867" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* plusp = false; */</span></span>
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3868
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<pre style="margin: 0;">+<span id="LC3868" class="line" lang="c"> </span>
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3869
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<pre style="margin: 0;">+<span id="LC3869" class="line" lang="c"> <span class="n" style="color: #333;">nexons</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Transcriptome_exons</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">exonbounds</span><span class="p">,</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">exonstarts</span><span class="p">,</span><span class="n" style="color: #333;">transcriptome</span><span class="p">,</span><span class="n" style="color: #333;">trnum</span><span class="p">);</span></span>
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3870
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<pre style="margin: 0;">+<span id="LC3870" class="line" lang="c"> <span class="n" style="color: #333;">Univ_IIT_interval_bounds</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">chroffset</span><span class="p">,</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">chrhigh</span><span class="p">,</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">chrlength</span><span class="p">,</span><span class="n" style="color: #333;">chromosome_iit</span><span class="p">,</span><span class="n" style="color: #333;">chrnum</span><span class="p">,</span><span class="n" style="color: #333;">circular_typeint</span><span class="p">);</span></span>
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3783
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3871
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<pre style="margin: 0;"> <span id="LC3871" class="line" lang="c"></span>
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3784
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<td class="diff-line-num new_line old" data-linenumber="3872" 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="LC3784" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">exoni</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">nexons</span><span class="p">)</span> <span class="p">{</span></span>
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3785
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<pre style="margin: 0;">-<span id="LC3785" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"ABORTING BECAUSE OF EXONI %d >= NEXONS %d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">exoni</span><span class="p">,</span><span class="n" style="color: #333;">nexons</span><span class="p">));</span></span>
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3872
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<pre style="margin: 0;">+<span id="LC3872" class="line" lang="c"> <span class="n" style="color: #333;">endpoints</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">Uintlist_T</span><span class="p">)</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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3873
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<pre style="margin: 0;">+<span id="LC3873" class="line" lang="c"> <span class="n" style="color: #333;">gaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">Intlist_T</span><span class="p">)</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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3874
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<pre style="margin: 0;">+<span id="LC3874" class="line" lang="c"> <span class="n" style="color: #333;">abortp</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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3875
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<pre style="margin: 0;">+<span id="LC3875" class="line" lang="c"> </span>
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3876
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<pre style="margin: 0;">+<span id="LC3876" class="line" lang="c"> <span class="n" style="color: #333;">transcript_diag0</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tr_left0</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">troffset</span><span class="p">;</span></span>
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3877
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<pre style="margin: 0;">+<span id="LC3877" class="line" lang="c"> <span class="n" style="color: #333;">transcript_diag1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tr_left1</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">troffset</span><span class="p">;</span></span>
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3878
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<pre style="margin: 0;">+<span id="LC3878" class="line" lang="c"> </span>
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3879
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<pre style="margin: 0;">+<span id="LC3879" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* first part */</span></span>
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3880
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<pre style="margin: 0;">+<span id="LC3880" class="line" lang="c"> <span class="n" style="color: #333;">tr_left</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tr_left0</span><span class="p">;</span></span>
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3881
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<pre style="margin: 0;">+<span id="LC3881" class="line" lang="c"> <span class="n" style="color: #333;">querystart</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/* tplus: compute from querystart to queryend */</span></span>
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3882
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<pre style="margin: 0;">+<span id="LC3882" class="line" lang="c"> <span class="n" style="color: #333;">queryend</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">indel_pos</span><span class="p">;</span></span>
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3883
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<pre style="margin: 0;">+<span id="LC3883" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</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;">Analyzing query %d..%d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">querystart</span><span class="p">,</span><span class="n" style="color: #333;">queryend</span><span class="p">));</span></span>
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3884
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<pre style="margin: 0;">+<span id="LC3884" class="line" lang="c"> </span>
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3885
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<pre style="margin: 0;">+<span id="LC3885" class="line" lang="c"> <span class="n" style="color: #333;">overall_trstart</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">trstart</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">transcript_diag0</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">querystart</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/* tplus */</span></span>
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3886
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<pre style="margin: 0;">+<span id="LC3886" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifdef DEBUG2</span></span>
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3887
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<pre style="margin: 0;">+<span id="LC3887" class="line" lang="c"> <span class="n" style="color: #333;">trend</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">transcript_diag0</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">queryend</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/* tplus */</span></span>
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3888
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<pre style="margin: 0;">+<span id="LC3888" class="line" lang="c"> <span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"transcript_diag %d, trstart %d, trend %d, tr_left %u, adj %d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span></span>
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3889
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<pre style="margin: 0;">+<span id="LC3889" class="line" lang="c"> <span class="n" style="color: #333;">transcript_diag0</span><span class="p">,</span><span class="n" style="color: #333;">trstart</span><span class="p">,</span><span class="n" style="color: #333;">trend</span><span class="p">,</span><span class="n" style="color: #333;">tr_left</span><span class="p">,</span><span class="n" style="color: #333;">adj</span><span class="p">);</span></span>
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3890
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<pre style="margin: 0;">+<span id="LC3890" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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3891
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<pre style="margin: 0;">+<span id="LC3891" class="line" lang="c"> </span>
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3892
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<pre style="margin: 0;">+<span id="LC3892" class="line" lang="c"> <span class="n" style="color: #333;">exoni</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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3893
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<pre style="margin: 0;">+<span id="LC3893" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;">#if 0 && defined(HAVE_AVX2)</span></span>
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3894
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<pre style="margin: 0;">+<span id="LC3894" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> _trstart = _mm256_set1_epi32(trstart);</span></span>
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3895
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<pre style="margin: 0;">+<span id="LC3895" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> ptr = exonbounds;</span></span>
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3896
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<pre style="margin: 0;">+<span id="LC3896" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> _exonbounds = _mm256_loadu_si256((__m256i *) ptr);</span></span>
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3897
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<pre style="margin: 0;">+<span id="LC3897" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> _diff = _mm256_cmpgt_epi32(_exonbounds,_trstart);</span></span>
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3898
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<pre style="margin: 0;">+<span id="LC3898" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> while (all_zero_p(_diff)) {</span></span>
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3899
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<pre style="margin: 0;">+<span id="LC3899" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> exoni += 8;</span></span>
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3900
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<pre style="margin: 0;">+<span id="LC3900" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> ptr += 8;</span></span>
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3901
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<pre style="margin: 0;">+<span id="LC3901" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> _exonbounds = _mm256_loadu_si256((__m256i *) ptr);</span></span>
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3902
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<pre style="margin: 0;">+<span id="LC3902" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> _diff = _mm256_cmpgt_epi32(_exonbounds,_trstart);</span></span>
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3903
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<pre style="margin: 0;">+<span id="LC3903" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> }</span></span>
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3904
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<pre style="margin: 0;">+<span id="LC3904" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> matchbits = _mm256_movemask_ps(_mm256_castsi256_ps(_diff));</span></span>
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3905
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<pre style="margin: 0;">+<span id="LC3905" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> exoni += count_trailing_zeroes_32(matchbits);</span></span>
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3906
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<pre style="margin: 0;">+<span id="LC3906" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;">#elif</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">defined</span><span class="p">(</span><span class="n" style="color: #333;">HAVE_SSE2</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3907" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3907
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<pre style="margin: 0;">+<span id="LC3907" class="line" lang="c"> <span class="n" style="color: #333;">_trstart</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_set1_epi32</span><span class="p">(</span><span class="n" style="color: #333;">trstart</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3908" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3908
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<pre style="margin: 0;">+<span id="LC3908" class="line" lang="c"> <span class="n" style="color: #333;">ptr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">exonbounds</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3909" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3909
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<pre style="margin: 0;">+<span id="LC3909" class="line" lang="c"> <span class="n" style="color: #333;">_exonbounds</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_loadu_si128</span><span class="p">((</span><span class="n" style="color: #333;">__m128i</span> <span class="o" style="font-weight: 600;">*</span><span class="p">)</span> <span class="n" style="color: #333;">ptr</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3910" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3910
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<pre style="margin: 0;">+<span id="LC3910" class="line" lang="c"> <span class="n" style="color: #333;">_diff</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_cmpgt_epi32</span><span class="p">(</span><span class="n" style="color: #333;">_exonbounds</span><span class="p">,</span><span class="n" style="color: #333;">_trstart</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3911" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3911
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<pre style="margin: 0;">+<span id="LC3911" class="line" lang="c"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">all_zero_p</span><span class="p">(</span><span class="n" style="color: #333;">_diff</span><span class="p">))</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3912" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3912
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<pre style="margin: 0;">+<span id="LC3912" class="line" lang="c"> <span class="n" style="color: #333;">exoni</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">4</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3913" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3913
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<pre style="margin: 0;">+<span id="LC3913" class="line" lang="c"> <span class="n" style="color: #333;">ptr</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">4</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3914" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3914
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<pre style="margin: 0;">+<span id="LC3914" class="line" lang="c"> <span class="n" style="color: #333;">_exonbounds</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_loadu_si128</span><span class="p">((</span><span class="n" style="color: #333;">__m128i</span> <span class="o" style="font-weight: 600;">*</span><span class="p">)</span> <span class="n" style="color: #333;">ptr</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3915" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3915
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<pre style="margin: 0;">+<span id="LC3915" class="line" lang="c"> <span class="n" style="color: #333;">_diff</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_cmpgt_epi32</span><span class="p">(</span><span class="n" style="color: #333;">_exonbounds</span><span class="p">,</span><span class="n" style="color: #333;">_trstart</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3916" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3916
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<pre style="margin: 0;">+<span id="LC3916" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3917" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3917
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<pre style="margin: 0;">+<span id="LC3917" class="line" lang="c"> <span class="n" style="color: #333;">matchbits</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_movemask_ps</span><span class="p">(</span><span class="n" style="color: #333;">_mm_castsi128_ps</span><span class="p">(</span><span class="n" style="color: #333;">_diff</span><span class="p">));</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3918" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3918
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<pre style="margin: 0;">+<span id="LC3918" class="line" lang="c"> <span class="n" style="color: #333;">exoni</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">count_trailing_zeroes_32</span><span class="p">(</span><span class="n" style="color: #333;">matchbits</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3919" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3919
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<pre style="margin: 0;">+<span id="LC3919" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#else</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3920" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3920
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<pre style="margin: 0;">+<span id="LC3920" class="line" lang="c"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">exoni</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">nexons</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">exonbounds</span><span class="p">[</span><span class="n" style="color: #333;">exoni</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">trstart</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3921" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3921
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<pre style="margin: 0;">+<span id="LC3921" class="line" lang="c"> <span class="n" style="color: #333;">exoni</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3922" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3922
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<pre style="margin: 0;">+<span id="LC3922" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3923" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3923
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<pre style="margin: 0;">+<span id="LC3923" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3924" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3924
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<pre style="margin: 0;">+<span id="LC3924" class="line" lang="c"> </span>
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<td class="diff-line-num new new_line" data-linenumber="3925" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3925
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<pre style="margin: 0;">+<span id="LC3925" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">exoni</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">nexons</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3926" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3926
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<pre style="margin: 0;">+<span id="LC3926" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"ABORTING BECAUSE OF EXONI %d >= NEXONS %d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">exoni</span><span class="p">,</span><span class="n" style="color: #333;">nexons</span><span class="p">));</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3927" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3927
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<pre style="margin: 0;">+<span id="LC3927" class="line" lang="c"> <span class="n" style="color: #333;">abortp</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3928" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3928
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<pre style="margin: 0;">+<span id="LC3928" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3929" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3929
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<pre style="margin: 0;">+<span id="LC3929" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"(11) exoni %d out of nexons %d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">exoni</span><span class="p">,</span><span class="n" style="color: #333;">nexons</span><span class="p">));</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3930" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3930
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<pre style="margin: 0;">+<span id="LC3930" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">exoni</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3931" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3931
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<pre style="margin: 0;">+<span id="LC3931" class="line" lang="c"> <span class="n" style="color: #333;">exonpos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">trstart</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3932" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3932
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<pre style="margin: 0;">+<span id="LC3932" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3933" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3933
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<pre style="margin: 0;">+<span id="LC3933" class="line" lang="c"> <span class="n" style="color: #333;">exonpos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">trstart</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">exonbounds</span><span class="p">[</span><span class="n" style="color: #333;">exoni</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">];</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3934" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3934
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<pre style="margin: 0;">+<span id="LC3934" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3935" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3935
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<pre style="margin: 0;">+<span id="LC3935" class="line" lang="c"> <span class="n" style="color: #333;">exon_residual</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">exonbounds</span><span class="p">[</span><span class="n" style="color: #333;">exoni</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">trstart</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3936" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3936
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<pre style="margin: 0;">+<span id="LC3936" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"exoni %d => exon_residual %d, exonpos %d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">exoni</span><span class="p">,</span><span class="n" style="color: #333;">exon_residual</span><span class="p">,</span><span class="n" style="color: #333;">exonpos</span><span class="p">));</span></span>
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3937
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<pre style="margin: 0;">+<span id="LC3937" class="line" lang="c"> </span>
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<td class="diff-line-num new new_line" data-linenumber="3938" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3938
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<pre style="margin: 0;">+<span id="LC3938" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Generate one substring per exon */</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3939" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3939
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<pre style="margin: 0;">+<span id="LC3939" class="line" lang="c"> <span class="n" style="color: #333;">genomicpos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">exonstarts</span><span class="p">[</span><span class="n" style="color: #333;">exoni</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">exonpos</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/* gminus */</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3940" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3940
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<pre style="margin: 0;">+<span id="LC3940" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"genomicpos %u = %u - %u</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">genomicpos</span><span class="p">,</span><span class="n" style="color: #333;">exonstarts</span><span class="p">[</span><span class="n" style="color: #333;">exoni</span><span class="p">],</span><span class="n" style="color: #333;">exonpos</span><span class="p">));</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3941" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3941
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<pre style="margin: 0;">+<span id="LC3941" class="line" lang="c"> <span class="n" style="color: #333;">align_residual</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">queryend</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">querystart</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3942" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3942
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<pre style="margin: 0;">+<span id="LC3942" class="line" lang="c"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">align_residual</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3943" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3943
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<pre style="margin: 0;">+<span id="LC3943" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"abortp %d, align_residual %d, exon_residual %d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">abortp</span><span class="p">,</span><span class="n" style="color: #333;">align_residual</span><span class="p">,</span><span class="n" style="color: #333;">exon_residual</span><span class="p">));</span></span>
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3944
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<pre style="margin: 0;">+<span id="LC3944" class="line" lang="c"> <span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">align_residual</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">exon_residual</span><span class="p">)</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">align_residual</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">exon_residual</span><span class="p">;</span></span>
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3945
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<pre style="margin: 0;">+<span id="LC3945" class="line" lang="c"> <span class="n" style="color: #333;">queryend</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">querystart</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">len</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/* tplus */</span></span>
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3946
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<pre style="margin: 0;">+<span id="LC3946" class="line" lang="c"> </span>
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3947
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<pre style="margin: 0;">+<span id="LC3947" class="line" lang="c"> <span class="n" style="color: #333;">alignstart</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">chroffset</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">genomicpos</span><span class="p">;</span></span>
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3948
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<pre style="margin: 0;">+<span id="LC3948" class="line" lang="c"> <span class="n" style="color: #333;">alignend</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alignstart</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">len</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/* gminus */</span></span>
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3949
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<pre style="margin: 0;">+<span id="LC3949" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">left</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alignend</span> <span class="o" style="font-weight: 600;">-</span> <span class="p">(</span><span class="n" style="color: #333;">querylength</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">queryend</span><span class="p">));</span> <span class="cm" style="color: #998; font-style: italic;">/* tplus != gminus */</span></span>
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3950
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<pre style="margin: 0;">+<span id="LC3950" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"tr ultrafast gap case 2 1st part query %d..%d, align %u..%u [%u..%u], left %u = %u - (%d - %d)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span></span>
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3951
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<pre style="margin: 0;">+<span id="LC3951" class="line" lang="c"> <span class="n" style="color: #333;">querystart</span><span class="p">,</span><span class="n" style="color: #333;">queryend</span><span class="p">,</span><span class="n" style="color: #333;">alignstart</span><span class="p">,</span><span class="n" style="color: #333;">alignend</span><span class="p">,</span><span class="n" style="color: #333;">alignstart</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">chroffset</span><span class="p">,</span><span class="n" style="color: #333;">alignend</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">chroffset</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3952" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3952
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<pre style="margin: 0;">+<span id="LC3952" class="line" lang="c"> <span class="n" style="color: #333;">left</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">chroffset</span><span class="p">,</span><span class="n" style="color: #333;">alignend</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">chroffset</span><span class="p">,</span><span class="n" style="color: #333;">querylength</span><span class="p">,</span><span class="n" style="color: #333;">queryend</span><span class="p">));</span></span>
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3953
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<pre style="margin: 0;">+<span id="LC3953" class="line" lang="c"> </span>
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3954
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<pre style="margin: 0;">+<span id="LC3954" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* tplus: push alignstart first */</span></span>
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3955
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<pre style="margin: 0;">+<span id="LC3955" class="line" lang="c"> <span class="n" style="color: #333;">endpoints</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Uintlist_push</span><span class="p">(</span><span class="n" style="color: #333;">endpoints</span><span class="p">,(</span><span class="n" style="color: #333;">Chrpos_T</span><span class="p">)</span> <span class="p">(</span><span class="n" style="color: #333;">alignstart</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">chroffset</span><span class="p">));</span></span>
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3956
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<pre style="margin: 0;">+<span id="LC3956" class="line" lang="c"> <span class="n" style="color: #333;">endpoints</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Uintlist_push</span><span class="p">(</span><span class="n" style="color: #333;">endpoints</span><span class="p">,(</span><span class="n" style="color: #333;">Chrpos_T</span><span class="p">)</span> <span class="p">(</span><span class="n" style="color: #333;">alignend</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">chroffset</span><span class="p">));</span></span>
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3957
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<pre style="margin: 0;">+<span id="LC3957" class="line" lang="c"> </span>
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3958
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<pre style="margin: 0;">+<span id="LC3958" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">align_residual</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">exon_residual</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3959" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3959
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<pre style="margin: 0;">+<span id="LC3959" class="line" lang="c"> <span class="n" style="color: #333;">exon_residual</span> <span class="o" style="font-weight: 600;">-=</span> <span class="n" style="color: #333;">align_residual</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/* Need to know this if we have a following deletion */</span></span>
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3960
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<pre style="margin: 0;">+<span id="LC3960" class="line" lang="c"> <span class="n" style="color: #333;">align_residual</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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3961
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<pre style="margin: 0;">+<span id="LC3961" class="line" lang="c"> <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="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">exoni</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">nexons</span><span class="p">)</span> <span class="p">{</span></span>
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3962
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<pre style="margin: 0;">+<span id="LC3962" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Aligning past the end of the transcript */</span></span>
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3963
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<pre style="margin: 0;">+<span id="LC3963" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"4 ABORTING BECAUSE ALIGNING PAST END OF TRANSCRIPT</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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3964
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<pre style="margin: 0;">+<span id="LC3964" class="line" lang="c"> <span class="n" style="color: #333;">align_residual</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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3786
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3965
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<pre style="margin: 0;"> <span id="LC3965" class="line" lang="c"> <span class="n" style="color: #333;">abortp</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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3787
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3966
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<pre style="margin: 0;"> <span id="LC3966" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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3788
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<td class="diff-line-num new_line old" data-linenumber="3967" 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="LC3788" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"(10) exoni %d out of nexons %d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">exoni</span><span class="p">,</span><span class="n" style="color: #333;">nexons</span><span class="p">));</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3789" 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">
3789
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<td class="diff-line-num new_line old" data-linenumber="3967" 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="LC3789" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">exoni</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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3790
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<td class="diff-line-num new_line old" data-linenumber="3967" 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="LC3790" class="line" lang="c"> <span class="n" style="color: #333;">exonpos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">trstart</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3791" 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">
3791
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<td class="diff-line-num new_line old" data-linenumber="3967" 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="LC3791" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3792" 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">
3792
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<td class="diff-line-num new_line old" data-linenumber="3967" 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="LC3792" class="line" lang="c"> <span class="n" style="color: #333;">exonpos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">trstart</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">exonbounds</span><span class="p">[</span><span class="n" style="color: #333;">exoni</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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3793
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<td class="diff-line-num new_line old" data-linenumber="3967" 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="LC3793" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3794" 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">
3794
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<td class="diff-line-num new_line old" data-linenumber="3967" 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="LC3794" class="line" lang="c"> <span class="n" style="color: #333;">exon_residual</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">exonbounds</span><span class="p">[</span><span class="n" style="color: #333;">exoni</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">trstart</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3795" 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">
3795
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<td class="diff-line-num new_line old" data-linenumber="3967" 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="LC3795" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"exoni %d => exon_residual %d, exonpos %d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">exoni</span><span class="p">,</span><span class="n" style="color: #333;">exon_residual</span><span class="p">,</span><span class="n" style="color: #333;">exonpos</span><span class="p">));</span></span>
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3796
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<td class="diff-line-num new_line old" data-linenumber="3967" 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="LC3796" class="line" lang="c"></span>
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<td class="diff-line-num old old_line" data-linenumber="3797" 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">
3797
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<td class="diff-line-num new_line old" data-linenumber="3967" 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="LC3797" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Generate one substring per exon */</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3798" 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">
3798
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<td class="diff-line-num new_line old" data-linenumber="3967" 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="LC3798" class="line" lang="c"> <span class="n" style="color: #333;">genomicpos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">exonstarts</span><span class="p">[</span><span class="n" style="color: #333;">exoni</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">exonpos</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/* gplus */</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3799" 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">
3799
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<td class="diff-line-num new_line old" data-linenumber="3967" 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="LC3799" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"genomicpos %u = %u + %u - 1</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">genomicpos</span><span class="p">,</span><span class="n" style="color: #333;">exonstarts</span><span class="p">[</span><span class="n" style="color: #333;">exoni</span><span class="p">],</span><span class="n" style="color: #333;">exonpos</span><span class="p">));</span></span>
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3800
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<td class="diff-line-num new_line old" data-linenumber="3967" 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="LC3800" class="line" lang="c"> <span class="n" style="color: #333;">align_residual</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">queryend</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">querystart</span><span class="p">;</span></span>
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3801
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<td class="diff-line-num new_line old" data-linenumber="3967" 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="LC3801" class="line" lang="c"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">align_residual</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3802" 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">
3802
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<td class="diff-line-num new_line old" data-linenumber="3967" 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="LC3802" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"abortp %d, align_residual %d, exon_residual %d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">abortp</span><span class="p">,</span><span class="n" style="color: #333;">align_residual</span><span class="p">,</span><span class="n" style="color: #333;">exon_residual</span><span class="p">));</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3803" 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">
3803
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<td class="diff-line-num new_line old" data-linenumber="3967" 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="LC3803" class="line" lang="c"> <span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">align_residual</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">exon_residual</span><span class="p">)</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">align_residual</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">exon_residual</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3804" 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">
3804
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<td class="diff-line-num new_line old" data-linenumber="3967" 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="LC3804" class="line" lang="c"> <span class="n" style="color: #333;">queryend</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">querystart</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">len</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/* tplus */</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3805" 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">
3805
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<pre style="margin: 0;">-<span id="LC3805" class="line" lang="c"> </span>
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<td class="diff-line-num old old_line" data-linenumber="3806" 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">
3806
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<pre style="margin: 0;">-<span id="LC3806" class="line" lang="c"> <span class="n" style="color: #333;">alignstart</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">chroffset</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">genomicpos</span><span class="p">;</span></span>
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3807
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<td class="diff-line-num new_line old" data-linenumber="3967" 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="LC3807" class="line" lang="c"> <span class="n" style="color: #333;">alignend</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alignstart</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">len</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/* gplus */</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3808" 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">
3808
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<td class="diff-line-num new_line old" data-linenumber="3967" 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="LC3808" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">left</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alignstart</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">querystart</span><span class="p">);</span> <span class="cm" style="color: #998; font-style: italic;">/* tplus == gminus */</span></span>
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3809
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<td class="diff-line-num new_line old" data-linenumber="3967" 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="LC3809" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"tr ultrafast gap case 1 2nd part query %d..%d, align %u..%u [%u..%u], left %u = %u - %d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3810" 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">
3810
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<td class="diff-line-num new_line old" data-linenumber="3967" 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="LC3810" class="line" lang="c"> <span class="n" style="color: #333;">querystart</span><span class="p">,</span><span class="n" style="color: #333;">queryend</span><span class="p">,</span><span class="n" style="color: #333;">alignstart</span><span class="p">,</span><span class="n" style="color: #333;">alignend</span><span class="p">,</span><span class="n" style="color: #333;">alignstart</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">chroffset</span><span class="p">,</span><span class="n" style="color: #333;">alignend</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">chroffset</span><span class="p">,</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3811" 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">
3811
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<td class="diff-line-num new_line old" data-linenumber="3967" 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="LC3811" class="line" lang="c"> <span class="n" style="color: #333;">left</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">chroffset</span><span class="p">,</span><span class="n" style="color: #333;">alignstart</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">chroffset</span><span class="p">,</span><span class="n" style="color: #333;">querystart</span><span class="p">));</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3812" 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">
3812
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<td class="diff-line-num new_line old" data-linenumber="3967" 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="LC3812" class="line" lang="c"> </span>
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<td class="diff-line-num old old_line" data-linenumber="3813" 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">
3813
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<td class="diff-line-num new_line old" data-linenumber="3967" 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="LC3813" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* tplus: push alignstart first */</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3814" 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">
3814
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<td class="diff-line-num new_line old" data-linenumber="3967" 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="LC3814" class="line" lang="c"> <span class="n" style="color: #333;">endpoints</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Uintlist_push</span><span class="p">(</span><span class="n" style="color: #333;">endpoints</span><span class="p">,(</span><span class="n" style="color: #333;">Chrpos_T</span><span class="p">)</span> <span class="p">(</span><span class="n" style="color: #333;">alignstart</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">chroffset</span><span class="p">));</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3815" 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">
3815
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<td class="diff-line-num new_line old" data-linenumber="3967" 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="LC3815" class="line" lang="c"> <span class="n" style="color: #333;">endpoints</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Uintlist_push</span><span class="p">(</span><span class="n" style="color: #333;">endpoints</span><span class="p">,(</span><span class="n" style="color: #333;">Chrpos_T</span><span class="p">)</span> <span class="p">(</span><span class="n" style="color: #333;">alignend</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">chroffset</span><span class="p">));</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3816" 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">
3816
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<pre style="margin: 0;">-<span id="LC3816" class="line" lang="c"></span>
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<td class="diff-line-num old old_line" data-linenumber="3817" 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">
3817
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<td class="diff-line-num new_line old" data-linenumber="3967" 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="LC3817" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">align_residual</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">exon_residual</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3818" 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">
3818
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<td class="diff-line-num new_line old" data-linenumber="3967" 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="LC3818" class="line" lang="c"> <span class="n" style="color: #333;">exon_residual</span> <span class="o" style="font-weight: 600;">-=</span> <span class="n" style="color: #333;">align_residual</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/* Need to know this if we have a following deletion */</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3819" 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">
3819
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<td class="diff-line-num new_line old" data-linenumber="3967" 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="LC3819" class="line" lang="c"> <span class="n" style="color: #333;">align_residual</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3820" 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">
3820
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<td class="diff-line-num new_line old" data-linenumber="3967" 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="LC3820" class="line" lang="c"> <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="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">exoni</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">nexons</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3821" 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">
3821
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<td class="diff-line-num new_line old" data-linenumber="3967" 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="LC3821" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Aligning past the end of the transcript */</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3822" 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">
3822
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<td class="diff-line-num new_line old" data-linenumber="3967" 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="LC3822" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"2 ABORTING BECAUSE ALIGNING PAST END OF TRANSCRIPT</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">));</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3823" 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">
3823
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<pre style="margin: 0;">-<span id="LC3823" class="line" lang="c"> <span class="n" style="color: #333;">align_residual</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3824" 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">
3824
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<pre style="margin: 0;">-<span id="LC3824" class="line" lang="c"> <span class="n" style="color: #333;">abortp</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3825" 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">
3825
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<td class="diff-line-num new_line old" data-linenumber="3967" 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="LC3825" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3826" 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">
3826
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<pre style="margin: 0;">-<span id="LC3826" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* nintrons += 1; */</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3827" 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">
3827
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<pre style="margin: 0;">-<span id="LC3827" class="line" lang="c"> <span class="n" style="color: #333;">align_residual</span> <span class="o" style="font-weight: 600;">-=</span> <span class="n" style="color: #333;">len</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3828" 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">
3828
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<td class="diff-line-num new_line old" data-linenumber="3967" 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="LC3828" class="line" lang="c"> <span class="n" style="color: #333;">querystart</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">len</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/* tplus */</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3829" 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">
3829
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<td class="diff-line-num new_line old" data-linenumber="3967" 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="LC3829" class="line" lang="c"> <span class="n" style="color: #333;">genomicpos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">exonstarts</span><span class="p">[</span><span class="n" style="color: #333;">exoni</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="cm" style="color: #998; font-style: italic;">/* gplus */</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3830" 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">
3830
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<td class="diff-line-num new_line old" data-linenumber="3967" 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="LC3830" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"genomicpos %u = %u - 1</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">genomicpos</span><span class="p">,</span><span class="n" style="color: #333;">exonstarts</span><span class="p">[</span><span class="n" style="color: #333;">exoni</span><span class="p">]));</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3831" 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">
3831
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<td class="diff-line-num new_line old" data-linenumber="3967" 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="LC3831" class="line" lang="c"> <span class="n" style="color: #333;">exon_residual</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">exonbounds</span><span class="p">[</span><span class="n" style="color: #333;">exoni</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">exonbounds</span><span class="p">[</span><span class="n" style="color: #333;">exoni</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 old old_line" data-linenumber="3832" 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">
3832
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<td class="diff-line-num new_line old" data-linenumber="3967" 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="LC3832" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"INTRON</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">));</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3833" 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">
3833
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<td class="diff-line-num new_line old" data-linenumber="3967" 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="LC3833" class="line" lang="c"> <span class="n" style="color: #333;">gaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Intlist_push</span><span class="p">(</span><span class="n" style="color: #333;">gaps</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="3834" 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">
3834
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<td class="diff-line-num new_line old" data-linenumber="3967" 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="LC3834" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3835" 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">
3835
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<td class="diff-line-num new_line old" data-linenumber="3967" 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="LC3835" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3836" 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">
3836
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<td class="diff-line-num new_line old" data-linenumber="3967" 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="LC3836" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3837" 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">
3837
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<td class="diff-line-num new_line old" data-linenumber="3967" 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="LC3837" class="line" lang="c"></span>
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<td class="diff-line-num old old_line" data-linenumber="3838" 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">
3838
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<td class="diff-line-num new_line old" data-linenumber="3967" 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="LC3838" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">abortp</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3839" 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">
3839
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<td class="diff-line-num new_line old" data-linenumber="3967" 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="LC3839" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"ABORTING PATH</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">));</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3840" 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">
3840
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<td class="diff-line-num new_line old" data-linenumber="3967" 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="LC3840" class="line" lang="c"> <span class="n" style="color: #333;">Uintlist_free</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">endpoints</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3841" 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">
3841
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<td class="diff-line-num new_line old" data-linenumber="3967" 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="LC3841" class="line" lang="c"> <span class="n" style="color: #333;">Intlist_free</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">gaps</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3842" 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">
3842
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<td class="diff-line-num new_line old" data-linenumber="3967" 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="LC3842" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3843" 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">
3843
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<td class="diff-line-num new_line old" data-linenumber="3967" 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="LC3843" class="line" lang="c"> <span class="n" style="color: #333;">endpoints</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Uintlist_reverse</span><span class="p">(</span><span class="n" style="color: #333;">endpoints</span><span class="p">);</span> <span class="cm" style="color: #998; font-style: italic;">/* gplus */</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3844" 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">
3844
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<td class="diff-line-num new_line old" data-linenumber="3967" 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="LC3844" class="line" lang="c"> <span class="n" style="color: #333;">gaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Intlist_reverse</span><span class="p">(</span><span class="n" style="color: #333;">gaps</span><span class="p">);</span> <span class="cm" style="color: #998; font-style: italic;">/* gplus */</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3845" 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">
3845
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<td class="diff-line-num new_line old" data-linenumber="3967" 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="LC3845" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"PLUS PATH %d. ENDPOINTS: %s. GAPS: %s</span><span class="se" style="color: #d14;">\n\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3846" 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">
3846
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<td class="diff-line-num new_line old" data-linenumber="3967" 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="LC3846" class="line" lang="c"> <span class="n" style="color: #333;">ngplus</span><span class="p">,</span><span class="n" style="color: #333;">Uintlist_to_string</span><span class="p">(</span><span class="n" style="color: #333;">endpoints</span><span class="p">),</span><span class="n" style="color: #333;">Intlist_to_string</span><span class="p">(</span><span class="n" style="color: #333;">gaps</span><span class="p">)));</span></span>
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3847
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<pre style="margin: 0;">-<span id="LC3847" class="line" lang="c"> <span class="n" style="color: #333;">gplus_paths</span><span class="p">[</span><span class="n" style="color: #333;">ngplus</span><span class="o" style="font-weight: 600;">++</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Path_new</span><span class="p">(</span><span class="n" style="color: #333;">total_nmatches</span><span class="p">,</span><span class="n" style="color: #333;">trnum</span><span class="p">,</span><span class="n" style="color: #333;">overall_trstart</span><span class="p">,</span><span class="n" style="color: #333;">overall_trend</span><span class="p">,</span></span>
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3848
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<td class="diff-line-num new_line old" data-linenumber="3967" 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="LC3848" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/*trim_low*/</span><span class="n" style="color: #333;">trim5</span><span class="p">,</span><span class="cm" style="color: #998; font-style: italic;">/*trim_high*/</span><span class="n" style="color: #333;">trim3</span><span class="p">,</span></span>
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3849
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<td class="diff-line-num new_line old" data-linenumber="3967" 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="LC3849" class="line" lang="c"> <span class="n" style="color: #333;">chrnum</span><span class="p">,</span><span class="n" style="color: #333;">chroffset</span><span class="p">,</span><span class="n" style="color: #333;">chrhigh</span><span class="p">,</span><span class="n" style="color: #333;">chrlength</span><span class="p">,</span><span class="n" style="color: #333;">endpoints</span><span class="p">,</span><span class="n" style="color: #333;">gaps</span><span class="p">,</span><span class="n" style="color: #333;">concordantp</span><span class="p">);</span></span>
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3967
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<pre style="margin: 0;">+<span id="LC3967" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* nintrons += 1; */</span></span>
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3968
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<pre style="margin: 0;">+<span id="LC3968" class="line" lang="c"> <span class="n" style="color: #333;">align_residual</span> <span class="o" style="font-weight: 600;">-=</span> <span class="n" style="color: #333;">len</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3969" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3969
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<pre style="margin: 0;">+<span id="LC3969" class="line" lang="c"> <span class="n" style="color: #333;">querystart</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">len</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/* tplus */</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3970" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3970
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<pre style="margin: 0;">+<span id="LC3970" class="line" lang="c"> <span class="n" style="color: #333;">genomicpos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">exonstarts</span><span class="p">[</span><span class="n" style="color: #333;">exoni</span><span class="p">];</span> <span class="cm" style="color: #998; font-style: italic;">/* gminus */</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3971" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3971
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<pre style="margin: 0;">+<span id="LC3971" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"genomicpos %u = %u</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">genomicpos</span><span class="p">,</span><span class="n" style="color: #333;">exonstarts</span><span class="p">[</span><span class="n" style="color: #333;">exoni</span><span class="p">]));</span></span>
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3972
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<pre style="margin: 0;">+<span id="LC3972" class="line" lang="c"> <span class="n" style="color: #333;">exon_residual</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">exonbounds</span><span class="p">[</span><span class="n" style="color: #333;">exoni</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">exonbounds</span><span class="p">[</span><span class="n" style="color: #333;">exoni</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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3973
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<pre style="margin: 0;">+<span id="LC3973" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"INTRON</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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3974
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<pre style="margin: 0;">+<span id="LC3974" class="line" lang="c"> <span class="n" style="color: #333;">gaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Intlist_push</span><span class="p">(</span><span class="n" style="color: #333;">gaps</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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3850
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3975
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<pre style="margin: 0;"> <span id="LC3975" class="line" lang="c"> <span class="p">}</span></span>
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3851
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<td class="diff-line-num new_line old" data-linenumber="3976" 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="LC3851" class="line" lang="c"></span>
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3852
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<pre style="margin: 0;">-<span id="LC3852" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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3853
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<td class="diff-line-num new_line old" data-linenumber="3976" 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="LC3853" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Case 2 ultrafast gap: tplus, gminus. transcript_plusp == true && transcript_genestrand < 0 */</span></span>
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3854
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<pre style="margin: 0;">-<span id="LC3854" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"Case 2 ultrafast gap: tplus, gminus</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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3855
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<pre style="margin: 0;">-<span id="LC3855" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* sensedir = SENSE_FORWARD; */</span></span>
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3856
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<pre style="margin: 0;">-<span id="LC3856" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* plusp = false; */</span></span>
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3857
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<pre style="margin: 0;">-<span id="LC3857" class="line" lang="c"> </span>
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3858
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<pre style="margin: 0;">-<span id="LC3858" class="line" lang="c"> <span class="n" style="color: #333;">endpoints</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">Uintlist_T</span><span class="p">)</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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3859
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<pre style="margin: 0;">-<span id="LC3859" class="line" lang="c"> <span class="n" style="color: #333;">gaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">Intlist_T</span><span class="p">)</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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3976
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<pre style="margin: 0;">+<span id="LC3976" class="line" lang="c"> <span class="p">}</span></span>
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3977
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<pre style="margin: 0;">+<span id="LC3977" class="line" lang="c"> <span class="p">}</span></span>
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3860
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3978
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<pre style="margin: 0;"> <span id="LC3978" class="line" lang="c"> </span>
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3861
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<pre style="margin: 0;">-<span id="LC3861" class="line" lang="c"> <span class="n" style="color: #333;">transcript_diag0</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tr_left0</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">troffset</span><span class="p">;</span></span>
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3862
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<td class="diff-line-num new_line old" data-linenumber="3979" 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="LC3862" class="line" lang="c"> <span class="n" style="color: #333;">transcript_diag1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tr_left1</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">troffset</span><span class="p">;</span></span>
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3863
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<pre style="margin: 0;">-<span id="LC3863" class="line" lang="c"></span>
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3864
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<td class="diff-line-num new_line old" data-linenumber="3979" 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="LC3864" class="line" lang="c"> <span class="n" style="color: #333;">abortp</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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3865
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<pre style="margin: 0;">-<span id="LC3865" class="line" lang="c"></span>
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3866
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<pre style="margin: 0;">-<span id="LC3866" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* first part */</span></span>
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3867
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<pre style="margin: 0;">-<span id="LC3867" class="line" lang="c"> <span class="n" style="color: #333;">tr_left</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tr_left0</span><span class="p">;</span></span>
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3868
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<pre style="margin: 0;">-<span id="LC3868" class="line" lang="c"> <span class="n" style="color: #333;">querystart</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/* tplus: compute from querystart to queryend */</span></span>
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3869
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<pre style="margin: 0;">-<span id="LC3869" class="line" lang="c"> <span class="n" style="color: #333;">queryend</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">indel_pos</span><span class="p">;</span></span>
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3870
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<pre style="margin: 0;">-<span id="LC3870" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</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;">Analyzing query %d..%d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">querystart</span><span class="p">,</span><span class="n" style="color: #333;">queryend</span><span class="p">));</span></span>
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3871
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<pre style="margin: 0;">-<span id="LC3871" class="line" lang="c"></span>
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3872
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<td class="diff-line-num new_line old" data-linenumber="3979" 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="LC3872" class="line" lang="c"> <span class="n" style="color: #333;">overall_trstart</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">trstart</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">transcript_diag0</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">querystart</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/* tplus */</span></span>
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3873
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<pre style="margin: 0;">-<span id="LC3873" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifdef DEBUG2</span></span>
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3874
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<td class="diff-line-num new_line old" data-linenumber="3979" 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="LC3874" class="line" lang="c"> <span class="n" style="color: #333;">trend</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">transcript_diag0</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">queryend</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/* tplus */</span></span>
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3875
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<td class="diff-line-num new_line old" data-linenumber="3979" 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="LC3875" class="line" lang="c"> <span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"transcript_diag %d, trstart %d, trend %d, tr_left %u, adj %d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span></span>
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3876
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<td class="diff-line-num new_line old" data-linenumber="3979" 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="LC3876" class="line" lang="c"> <span class="n" style="color: #333;">transcript_diag0</span><span class="p">,</span><span class="n" style="color: #333;">trstart</span><span class="p">,</span><span class="n" style="color: #333;">trend</span><span class="p">,</span><span class="n" style="color: #333;">tr_left</span><span class="p">,</span><span class="n" style="color: #333;">adj</span><span class="p">);</span></span>
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3877
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<pre style="margin: 0;">-<span id="LC3877" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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3878
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<pre style="margin: 0;">-<span id="LC3878" class="line" lang="c"></span>
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3879
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<pre style="margin: 0;">-<span id="LC3879" class="line" lang="c"> <span class="n" style="color: #333;">exoni</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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3880
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<pre style="margin: 0;">-<span id="LC3880" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;">#if 0 && defined(HAVE_AVX2)</span></span>
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3881
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<td class="diff-line-num new_line old" data-linenumber="3979" 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="LC3881" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> _trstart = _mm256_set1_epi32(trstart);</span></span>
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3882
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<pre style="margin: 0;">-<span id="LC3882" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> ptr = exonbounds;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3883" 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">
3883
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<td class="diff-line-num new_line old" data-linenumber="3979" 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="LC3883" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> _exonbounds = _mm256_loadu_si256((__m256i *) ptr);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3884" 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">
3884
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<td class="diff-line-num new_line old" data-linenumber="3979" 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="LC3884" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> _diff = _mm256_cmpgt_epi32(_exonbounds,_trstart);</span></span>
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3885
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<td class="diff-line-num new_line old" data-linenumber="3979" 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="LC3885" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> while (all_zero_p(_diff)) {</span></span>
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3886
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<td class="diff-line-num new_line old" data-linenumber="3979" 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="LC3886" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> exoni += 8;</span></span>
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3887
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<td class="diff-line-num new_line old" data-linenumber="3979" 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="LC3887" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> ptr += 8;</span></span>
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3888
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<td class="diff-line-num new_line old" data-linenumber="3979" 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="LC3888" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> _exonbounds = _mm256_loadu_si256((__m256i *) ptr);</span></span>
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3889
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<td class="diff-line-num new_line old" data-linenumber="3979" 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="LC3889" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> _diff = _mm256_cmpgt_epi32(_exonbounds,_trstart);</span></span>
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3890
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<pre style="margin: 0;">-<span id="LC3890" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> }</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3891" 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">
3891
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<td class="diff-line-num new_line old" data-linenumber="3979" 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="LC3891" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> matchbits = _mm256_movemask_ps(_mm256_castsi256_ps(_diff));</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3892" 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">
3892
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<td class="diff-line-num new_line old" data-linenumber="3979" 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="LC3892" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> exoni += count_trailing_zeroes_32(matchbits);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3893" 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">
3893
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<pre style="margin: 0;">-<span id="LC3893" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;">#elif</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">defined</span><span class="p">(</span><span class="n" style="color: #333;">HAVE_SSE2</span><span class="p">)</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3894" 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">
3894
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<pre style="margin: 0;">-<span id="LC3894" class="line" lang="c"> <span class="n" style="color: #333;">_trstart</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_set1_epi32</span><span class="p">(</span><span class="n" style="color: #333;">trstart</span><span class="p">);</span></span>
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3895
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<td class="diff-line-num new_line old" data-linenumber="3979" 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="LC3895" class="line" lang="c"> <span class="n" style="color: #333;">ptr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">exonbounds</span><span class="p">;</span></span>
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3896
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<td class="diff-line-num new_line old" data-linenumber="3979" 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="LC3896" class="line" lang="c"> <span class="n" style="color: #333;">_exonbounds</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_loadu_si128</span><span class="p">((</span><span class="n" style="color: #333;">__m128i</span> <span class="o" style="font-weight: 600;">*</span><span class="p">)</span> <span class="n" style="color: #333;">ptr</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3897" 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">
3897
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<td class="diff-line-num new_line old" data-linenumber="3979" 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="LC3897" class="line" lang="c"> <span class="n" style="color: #333;">_diff</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_cmpgt_epi32</span><span class="p">(</span><span class="n" style="color: #333;">_exonbounds</span><span class="p">,</span><span class="n" style="color: #333;">_trstart</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3898" 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">
3898
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<pre style="margin: 0;">-<span id="LC3898" class="line" lang="c"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">all_zero_p</span><span class="p">(</span><span class="n" style="color: #333;">_diff</span><span class="p">))</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3899" 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">
3899
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<pre style="margin: 0;">-<span id="LC3899" class="line" lang="c"> <span class="n" style="color: #333;">exoni</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">4</span><span class="p">;</span></span>
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3900
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<pre style="margin: 0;">-<span id="LC3900" class="line" lang="c"> <span class="n" style="color: #333;">ptr</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">4</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3901" 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">
3901
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<pre style="margin: 0;">-<span id="LC3901" class="line" lang="c"> <span class="n" style="color: #333;">_exonbounds</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_loadu_si128</span><span class="p">((</span><span class="n" style="color: #333;">__m128i</span> <span class="o" style="font-weight: 600;">*</span><span class="p">)</span> <span class="n" style="color: #333;">ptr</span><span class="p">);</span></span>
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3902
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<pre style="margin: 0;">-<span id="LC3902" class="line" lang="c"> <span class="n" style="color: #333;">_diff</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_cmpgt_epi32</span><span class="p">(</span><span class="n" style="color: #333;">_exonbounds</span><span class="p">,</span><span class="n" style="color: #333;">_trstart</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3903" 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">
3903
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<td class="diff-line-num new_line old" data-linenumber="3979" 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="LC3903" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3904" 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">
3904
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<td class="diff-line-num new_line old" data-linenumber="3979" 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="LC3904" class="line" lang="c"> <span class="n" style="color: #333;">matchbits</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_movemask_ps</span><span class="p">(</span><span class="n" style="color: #333;">_mm_castsi128_ps</span><span class="p">(</span><span class="n" style="color: #333;">_diff</span><span class="p">));</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3905" 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">
3905
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<td class="diff-line-num new_line old" data-linenumber="3979" 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="LC3905" class="line" lang="c"> <span class="n" style="color: #333;">exoni</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">count_trailing_zeroes_32</span><span class="p">(</span><span class="n" style="color: #333;">matchbits</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3906" 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">
3906
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<td class="diff-line-num new_line old" data-linenumber="3979" 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="LC3906" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#else</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3907" 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">
3907
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<td class="diff-line-num new_line old" data-linenumber="3979" 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="LC3907" class="line" lang="c"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">exoni</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">nexons</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">exonbounds</span><span class="p">[</span><span class="n" style="color: #333;">exoni</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">trstart</span><span class="p">)</span> <span class="p">{</span></span>
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3908
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<td class="diff-line-num new_line old" data-linenumber="3979" 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="LC3908" class="line" lang="c"> <span class="n" style="color: #333;">exoni</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3909" 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">
3909
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<td class="diff-line-num new_line old" data-linenumber="3979" 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="LC3909" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3910" 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">
3910
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<td class="diff-line-num new_line old" data-linenumber="3979" 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="LC3910" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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3911
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<td class="diff-line-num new_line old" data-linenumber="3979" 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="LC3911" class="line" lang="c"></span>
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<td class="diff-line-num old old_line" data-linenumber="3912" 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">
3912
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<td class="diff-line-num new_line old" data-linenumber="3979" 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="LC3912" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">exoni</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">nexons</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3913" 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">
3913
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<td class="diff-line-num new_line old" data-linenumber="3979" 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="LC3913" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"ABORTING BECAUSE OF EXONI %d >= NEXONS %d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">exoni</span><span class="p">,</span><span class="n" style="color: #333;">nexons</span><span class="p">));</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3914" 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">
3914
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<td class="diff-line-num new_line old" data-linenumber="3979" 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="LC3914" class="line" lang="c"> <span class="n" style="color: #333;">abortp</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3915" 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">
3915
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<td class="diff-line-num new_line old" data-linenumber="3979" 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="LC3915" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3916" 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">
3916
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<td class="diff-line-num new_line old" data-linenumber="3979" 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="LC3916" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"(11) exoni %d out of nexons %d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">exoni</span><span class="p">,</span><span class="n" style="color: #333;">nexons</span><span class="p">));</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3917" 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">
3917
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<td class="diff-line-num new_line old" data-linenumber="3979" 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="LC3917" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">exoni</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3918" 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">
3918
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<td class="diff-line-num new_line old" data-linenumber="3979" 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="LC3918" class="line" lang="c"> <span class="n" style="color: #333;">exonpos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">trstart</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3919" 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">
3919
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<td class="diff-line-num new_line old" data-linenumber="3979" 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="LC3919" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3920" 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">
3920
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<td class="diff-line-num new_line old" data-linenumber="3979" 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="LC3920" class="line" lang="c"> <span class="n" style="color: #333;">exonpos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">trstart</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">exonbounds</span><span class="p">[</span><span class="n" style="color: #333;">exoni</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 old old_line" data-linenumber="3921" 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">
3921
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<td class="diff-line-num new_line old" data-linenumber="3979" 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="LC3921" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3922" 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">
3922
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<td class="diff-line-num new_line old" data-linenumber="3979" 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="LC3922" class="line" lang="c"> <span class="n" style="color: #333;">exon_residual</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">exonbounds</span><span class="p">[</span><span class="n" style="color: #333;">exoni</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">trstart</span><span class="p">;</span></span>
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3923
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<pre style="margin: 0;">-<span id="LC3923" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"exoni %d => exon_residual %d, exonpos %d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">exoni</span><span class="p">,</span><span class="n" style="color: #333;">exon_residual</span><span class="p">,</span><span class="n" style="color: #333;">exonpos</span><span class="p">));</span></span>
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3924
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<td class="diff-line-num new_line old" data-linenumber="3979" 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="LC3924" class="line" lang="c"></span>
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<td class="diff-line-num old old_line" data-linenumber="3925" 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">
3925
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<td class="diff-line-num new_line old" data-linenumber="3979" 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="LC3925" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Generate one substring per exon */</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3926" 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">
3926
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<td class="diff-line-num new_line old" data-linenumber="3979" 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="LC3926" class="line" lang="c"> <span class="n" style="color: #333;">genomicpos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">exonstarts</span><span class="p">[</span><span class="n" style="color: #333;">exoni</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">exonpos</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/* gminus */</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3927" 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">
3927
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<td class="diff-line-num new_line old" data-linenumber="3979" 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="LC3927" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"genomicpos %u = %u - %u</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">genomicpos</span><span class="p">,</span><span class="n" style="color: #333;">exonstarts</span><span class="p">[</span><span class="n" style="color: #333;">exoni</span><span class="p">],</span><span class="n" style="color: #333;">exonpos</span><span class="p">));</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3928" 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">
3928
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<td class="diff-line-num new_line old" data-linenumber="3979" 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="LC3928" class="line" lang="c"> <span class="n" style="color: #333;">align_residual</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">queryend</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">querystart</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3929" 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">
3929
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<td class="diff-line-num new_line old" data-linenumber="3979" 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="LC3929" class="line" lang="c"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">align_residual</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3930" 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">
3930
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<td class="diff-line-num new_line old" data-linenumber="3979" 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="LC3930" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"abortp %d, align_residual %d, exon_residual %d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">abortp</span><span class="p">,</span><span class="n" style="color: #333;">align_residual</span><span class="p">,</span><span class="n" style="color: #333;">exon_residual</span><span class="p">));</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3931" 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">
3931
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<td class="diff-line-num new_line old" data-linenumber="3979" 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="LC3931" class="line" lang="c"> <span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">align_residual</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">exon_residual</span><span class="p">)</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">align_residual</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">exon_residual</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3932" 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">
3932
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<td class="diff-line-num new_line old" data-linenumber="3979" 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="LC3932" class="line" lang="c"> <span class="n" style="color: #333;">queryend</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">querystart</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">len</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/* tplus */</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3933" 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">
3933
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<td class="diff-line-num new_line old" data-linenumber="3979" 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="LC3933" class="line" lang="c"></span>
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<td class="diff-line-num old old_line" data-linenumber="3934" 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">
3934
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<td class="diff-line-num new_line old" data-linenumber="3979" 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="LC3934" class="line" lang="c"> <span class="n" style="color: #333;">alignstart</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">chroffset</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">genomicpos</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3935" 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">
3935
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<td class="diff-line-num new_line old" data-linenumber="3979" 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="LC3935" class="line" lang="c"> <span class="n" style="color: #333;">alignend</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alignstart</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">len</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/* gminus */</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3936" 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">
3936
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<td class="diff-line-num new_line old" data-linenumber="3979" 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="LC3936" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">left</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alignend</span> <span class="o" style="font-weight: 600;">-</span> <span class="p">(</span><span class="n" style="color: #333;">querylength</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">queryend</span><span class="p">));</span> <span class="cm" style="color: #998; font-style: italic;">/* tplus != gminus */</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3937" 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">
3937
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<td class="diff-line-num new_line old" data-linenumber="3979" 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="LC3937" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"tr ultrafast gap case 2 1st part query %d..%d, align %u..%u [%u..%u], left %u = %u - (%d - %d)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3938" 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">
3938
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<td class="diff-line-num new_line old" data-linenumber="3979" 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="LC3938" class="line" lang="c"> <span class="n" style="color: #333;">querystart</span><span class="p">,</span><span class="n" style="color: #333;">queryend</span><span class="p">,</span><span class="n" style="color: #333;">alignstart</span><span class="p">,</span><span class="n" style="color: #333;">alignend</span><span class="p">,</span><span class="n" style="color: #333;">alignstart</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">chroffset</span><span class="p">,</span><span class="n" style="color: #333;">alignend</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">chroffset</span><span class="p">,</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3939" 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">
3939
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<td class="diff-line-num new_line old" data-linenumber="3979" 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="LC3939" class="line" lang="c"> <span class="n" style="color: #333;">left</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">chroffset</span><span class="p">,</span><span class="n" style="color: #333;">alignend</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">chroffset</span><span class="p">,</span><span class="n" style="color: #333;">querylength</span><span class="p">,</span><span class="n" style="color: #333;">queryend</span><span class="p">));</span></span>
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3940
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<pre style="margin: 0;">-<span id="LC3940" class="line" lang="c"></span>
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<td class="diff-line-num old old_line" data-linenumber="3941" 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">
3941
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<td class="diff-line-num new_line old" data-linenumber="3979" 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="LC3941" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* tplus: push alignstart first */</span></span>
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3942
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<pre style="margin: 0;">-<span id="LC3942" class="line" lang="c"> <span class="n" style="color: #333;">endpoints</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Uintlist_push</span><span class="p">(</span><span class="n" style="color: #333;">endpoints</span><span class="p">,(</span><span class="n" style="color: #333;">Chrpos_T</span><span class="p">)</span> <span class="p">(</span><span class="n" style="color: #333;">alignstart</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">chroffset</span><span class="p">));</span></span>
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3943
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<td class="diff-line-num new_line old" data-linenumber="3979" 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="LC3943" class="line" lang="c"> <span class="n" style="color: #333;">endpoints</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Uintlist_push</span><span class="p">(</span><span class="n" style="color: #333;">endpoints</span><span class="p">,(</span><span class="n" style="color: #333;">Chrpos_T</span><span class="p">)</span> <span class="p">(</span><span class="n" style="color: #333;">alignend</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">chroffset</span><span class="p">));</span></span>
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3944
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<pre style="margin: 0;">-<span id="LC3944" class="line" lang="c"></span>
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3945
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<td class="diff-line-num new_line old" data-linenumber="3979" 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="LC3945" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">align_residual</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">exon_residual</span><span class="p">)</span> <span class="p">{</span></span>
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3946
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<td class="diff-line-num new_line old" data-linenumber="3979" 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="LC3946" class="line" lang="c"> <span class="n" style="color: #333;">exon_residual</span> <span class="o" style="font-weight: 600;">-=</span> <span class="n" style="color: #333;">align_residual</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/* Need to know this if we have a following deletion */</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3947" 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">
3947
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<td class="diff-line-num new_line old" data-linenumber="3979" 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="LC3947" class="line" lang="c"> <span class="n" style="color: #333;">align_residual</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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3948
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<td class="diff-line-num new_line old" data-linenumber="3979" 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="LC3948" class="line" lang="c"> <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="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">exoni</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">nexons</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3949" 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">
3949
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<td class="diff-line-num new_line old" data-linenumber="3979" 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="LC3949" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Aligning past the end of the transcript */</span></span>
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3950
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<td class="diff-line-num new_line old" data-linenumber="3979" 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="LC3950" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"4 ABORTING BECAUSE ALIGNING PAST END OF TRANSCRIPT</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">));</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3951" 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">
3951
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<td class="diff-line-num new_line old" data-linenumber="3979" 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="LC3951" class="line" lang="c"> <span class="n" style="color: #333;">align_residual</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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3952
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<td class="diff-line-num new_line old" data-linenumber="3979" 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="LC3952" class="line" lang="c"> <span class="n" style="color: #333;">abortp</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3953" 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">
3953
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<td class="diff-line-num new_line old" data-linenumber="3979" 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="LC3953" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3954" 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">
3954
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<td class="diff-line-num new_line old" data-linenumber="3979" 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="LC3954" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* nintrons += 1; */</span></span>
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3955
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<td class="diff-line-num new_line old" data-linenumber="3979" 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="LC3955" class="line" lang="c"> <span class="n" style="color: #333;">align_residual</span> <span class="o" style="font-weight: 600;">-=</span> <span class="n" style="color: #333;">len</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3956" 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">
3956
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<td class="diff-line-num new_line old" data-linenumber="3979" 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="LC3956" class="line" lang="c"> <span class="n" style="color: #333;">querystart</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">len</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/* tplus */</span></span>
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3957
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<td class="diff-line-num new_line old" data-linenumber="3979" 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="LC3957" class="line" lang="c"> <span class="n" style="color: #333;">genomicpos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">exonstarts</span><span class="p">[</span><span class="n" style="color: #333;">exoni</span><span class="p">];</span> <span class="cm" style="color: #998; font-style: italic;">/* gminus */</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3958" 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">
3958
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<td class="diff-line-num new_line old" data-linenumber="3979" 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="LC3958" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"genomicpos %u = %u</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">genomicpos</span><span class="p">,</span><span class="n" style="color: #333;">exonstarts</span><span class="p">[</span><span class="n" style="color: #333;">exoni</span><span class="p">]));</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3959" 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">
3959
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<td class="diff-line-num new_line old" data-linenumber="3979" 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="LC3959" class="line" lang="c"> <span class="n" style="color: #333;">exon_residual</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">exonbounds</span><span class="p">[</span><span class="n" style="color: #333;">exoni</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">exonbounds</span><span class="p">[</span><span class="n" style="color: #333;">exoni</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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3960
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<td class="diff-line-num new_line old" data-linenumber="3979" 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="LC3960" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"INTRON</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">));</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3961" 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">
3961
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<pre style="margin: 0;">-<span id="LC3961" class="line" lang="c"> <span class="n" style="color: #333;">gaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Intlist_push</span><span class="p">(</span><span class="n" style="color: #333;">gaps</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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3962
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<pre style="margin: 0;">-<span id="LC3962" class="line" lang="c"> <span class="p">}</span></span>
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3963
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<td class="diff-line-num new_line old" data-linenumber="3979" 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="LC3963" class="line" lang="c"> <span class="p">}</span></span>
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3964
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<td class="diff-line-num new_line old" data-linenumber="3979" 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="LC3964" class="line" lang="c"> <span class="p">}</span></span>
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3965
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<td class="diff-line-num new_line old" data-linenumber="3979" 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="LC3965" class="line" lang="c"></span>
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<td class="diff-line-num old old_line" data-linenumber="3966" 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">
3966
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<td class="diff-line-num new_line old" data-linenumber="3979" 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="LC3966" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* gap */</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3967" 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">
3967
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<td class="diff-line-num new_line old" data-linenumber="3979" 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="LC3967" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"INDEL: last piece %d | nindels %d | next piece %d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">len</span><span class="p">,</span><span class="n" style="color: #333;">nindels</span><span class="p">,</span><span class="n" style="color: #333;">exon_residual</span><span class="p">));</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3968" 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">
3968
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<td class="diff-line-num new_line old" data-linenumber="3979" 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="LC3968" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"exon residual %d vs nindels %d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">exon_residual</span><span class="p">,</span><span class="n" style="color: #333;">nindels</span><span class="p">));</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3969" 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">
3969
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<td class="diff-line-num new_line old" data-linenumber="3979" 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="LC3969" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">abortp</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3970" 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">
3970
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<td class="diff-line-num new_line old" data-linenumber="3979" 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="LC3970" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Skip */</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3971" 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">
3971
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<td class="diff-line-num new_line old" data-linenumber="3979" 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="LC3971" class="line" lang="c"> <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="cm" style="color: #998; font-style: italic;">/*len <= nindels ||*/</span><span class="n" style="color: #333;">exon_residual</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">nindels</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3972" 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">
3972
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<td class="diff-line-num new_line old" data-linenumber="3979" 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="LC3972" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"ABORTING BECAUSE INDEL OVERLAPS SPLICE SITE</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">));</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3973" 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">
3973
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<td class="diff-line-num new_line old" data-linenumber="3979" 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="LC3973" class="line" lang="c"> <span class="n" style="color: #333;">abortp</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3974" 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">
3974
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<td class="diff-line-num new_line old" data-linenumber="3979" 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="LC3974" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3975" 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">
3975
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<td class="diff-line-num new_line old" data-linenumber="3979" 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="LC3975" class="line" lang="c"> <span class="n" style="color: #333;">gaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Intlist_push</span><span class="p">(</span><span class="n" style="color: #333;">gaps</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;">adj</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3976" 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">
3976
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<td class="diff-line-num new_line old" data-linenumber="3979" 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="LC3976" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3977" 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">
3977
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<td class="diff-line-num new_line old" data-linenumber="3979" 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="LC3977" class="line" lang="c"></span>
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<td class="diff-line-num old old_line" data-linenumber="3978" 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">
3978
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<td class="diff-line-num new_line old" data-linenumber="3979" 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="LC3978" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* second part */</span></span>
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3979
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<td class="diff-line-num new_line old" data-linenumber="3979" 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="LC3979" class="line" lang="c"> <span class="n" style="color: #333;">tr_left</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tr_left1</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3980" 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">
3980
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<td class="diff-line-num new_line old" data-linenumber="3979" 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="LC3980" class="line" lang="c"> <span class="n" style="color: #333;">querystart</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">indel_pos</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">ninserts</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3981" 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">
3981
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<td class="diff-line-num new_line old" data-linenumber="3979" 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="LC3981" class="line" lang="c"> <span class="n" style="color: #333;">queryend</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">querylength</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="3982" 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">
3982
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<td class="diff-line-num new_line old" data-linenumber="3979" 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="LC3982" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</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;">Analyzing query %d..%d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">querystart</span><span class="p">,</span><span class="n" style="color: #333;">queryend</span><span class="p">));</span></span>
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3983
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<td class="diff-line-num new_line old" data-linenumber="3979" 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="LC3983" class="line" lang="c"></span>
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<td class="diff-line-num old old_line" data-linenumber="3984" 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">
3984
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<pre style="margin: 0;">-<span id="LC3984" class="line" lang="c"> <span class="n" style="color: #333;">trstart</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">transcript_diag1</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">querystart</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/* tplus */</span></span>
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3985
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<pre style="margin: 0;">-<span id="LC3985" class="line" lang="c"> <span class="n" style="color: #333;">overall_trend</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">transcript_diag1</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">queryend</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/* tplus */</span></span>
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3986
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<pre style="margin: 0;">-<span id="LC3986" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"transcript_diag %d, trstart %d, trend %d, tr_left %u</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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3987
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<td class="diff-line-num new_line old" data-linenumber="3979" 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="LC3987" class="line" lang="c"> <span class="n" style="color: #333;">transcript_diag1</span><span class="p">,</span><span class="n" style="color: #333;">trstart</span><span class="p">,</span><span class="n" style="color: #333;">overall_trend</span><span class="p">,</span><span class="n" style="color: #333;">tr_left</span><span class="p">));</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3979" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3979
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<pre style="margin: 0;">+<span id="LC3979" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* gap */</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3980" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3980
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<pre style="margin: 0;">+<span id="LC3980" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"INDEL: last piece %d | nindels %d | next piece %d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">len</span><span class="p">,</span><span class="n" style="color: #333;">nindels</span><span class="p">,</span><span class="n" style="color: #333;">exon_residual</span><span class="p">));</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3981" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3981
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<pre style="margin: 0;">+<span id="LC3981" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"exon residual %d vs nindels %d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">exon_residual</span><span class="p">,</span><span class="n" style="color: #333;">nindels</span><span class="p">));</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3982" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3982
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<pre style="margin: 0;">+<span id="LC3982" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">abortp</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">)</span> <span class="p">{</span></span>
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3983
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<pre style="margin: 0;">+<span id="LC3983" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Skip */</span></span>
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3984
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<pre style="margin: 0;">+<span id="LC3984" class="line" lang="c"> <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="cm" style="color: #998; font-style: italic;">/*len <= nindels ||*/</span><span class="n" style="color: #333;">exon_residual</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">nindels</span><span class="p">)</span> <span class="p">{</span></span>
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3985
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<pre style="margin: 0;">+<span id="LC3985" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"ABORTING BECAUSE INDEL OVERLAPS SPLICE SITE (6)</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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3986
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<pre style="margin: 0;">+<span id="LC3986" class="line" lang="c"> <span class="n" style="color: #333;">abortp</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3987" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3987
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<pre style="margin: 0;">+<span id="LC3987" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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3988
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<pre style="margin: 0;">+<span id="LC3988" class="line" lang="c"> <span class="n" style="color: #333;">gaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Intlist_push</span><span class="p">(</span><span class="n" style="color: #333;">gaps</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;">adj</span><span class="p">);</span></span>
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3989
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<pre style="margin: 0;">+<span id="LC3989" class="line" lang="c"> <span class="p">}</span></span>
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3990
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<pre style="margin: 0;">+<span id="LC3990" class="line" lang="c"> </span>
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<td class="diff-line-num new new_line" data-linenumber="3991" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3991
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<pre style="margin: 0;">+<span id="LC3991" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* second part */</span></span>
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3992
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<pre style="margin: 0;">+<span id="LC3992" class="line" lang="c"> <span class="n" style="color: #333;">tr_left</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tr_left1</span><span class="p">;</span></span>
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3993
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<pre style="margin: 0;">+<span id="LC3993" class="line" lang="c"> <span class="n" style="color: #333;">querystart</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">indel_pos</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">ninserts</span><span class="p">;</span></span>
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3994
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<pre style="margin: 0;">+<span id="LC3994" class="line" lang="c"> <span class="n" style="color: #333;">queryend</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">querylength</span><span class="p">;</span></span>
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3995
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<pre style="margin: 0;">+<span id="LC3995" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</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;">Analyzing query %d..%d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">querystart</span><span class="p">,</span><span class="n" style="color: #333;">queryend</span><span class="p">));</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3996" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3996
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<pre style="margin: 0;">+<span id="LC3996" class="line" lang="c"> </span>
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<td class="diff-line-num new new_line" data-linenumber="3997" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3997
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<pre style="margin: 0;">+<span id="LC3997" class="line" lang="c"> <span class="n" style="color: #333;">trstart</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">transcript_diag1</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">querystart</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/* tplus */</span></span>
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3998
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<pre style="margin: 0;">+<span id="LC3998" class="line" lang="c"> <span class="n" style="color: #333;">overall_trend</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">transcript_diag1</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">queryend</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/* tplus */</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3999" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3999
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<pre style="margin: 0;">+<span id="LC3999" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"transcript_diag %d, trstart %d, trend %d, tr_left %u</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4000" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4000
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<pre style="margin: 0;">+<span id="LC4000" class="line" lang="c"> <span class="n" style="color: #333;">transcript_diag1</span><span class="p">,</span><span class="n" style="color: #333;">trstart</span><span class="p">,</span><span class="n" style="color: #333;">overall_trend</span><span class="p">,</span><span class="n" style="color: #333;">tr_left</span><span class="p">));</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4001" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4001
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<pre style="margin: 0;">+<span id="LC4001" class="line" lang="c"> </span>
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<td class="diff-line-num new old_line" data-linenumber="3988" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="4002" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4002
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<pre style="margin: 0;">+<span id="LC4002" class="line" lang="c"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">exoni</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">nexons</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">exonbounds</span><span class="p">[</span><span class="n" style="color: #333;">exoni</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">trstart</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4003" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4003
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<pre style="margin: 0;">+<span id="LC4003" class="line" lang="c"> <span class="n" style="color: #333;">exoni</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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4004
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<pre style="margin: 0;">+<span id="LC4004" class="line" lang="c"> <span class="p">}</span></span>
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4005
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<pre style="margin: 0;">+<span id="LC4005" class="line" lang="c"> </span>
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<td class="diff-line-num new new_line" data-linenumber="4006" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4006
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<pre style="margin: 0;">+<span id="LC4006" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">exoni</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">nexons</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4007" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4007
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<pre style="margin: 0;">+<span id="LC4007" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"ABORTING BECAUSE OF EXONI %d >= NEXONS %d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">exoni</span><span class="p">,</span><span class="n" style="color: #333;">nexons</span><span class="p">));</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4008" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4008
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<pre style="margin: 0;">+<span id="LC4008" class="line" lang="c"> <span class="n" style="color: #333;">abortp</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4009" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4009
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<pre style="margin: 0;">+<span id="LC4009" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4010" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4010
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<pre style="margin: 0;">+<span id="LC4010" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"(12) exoni %d out of nexons %d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">exoni</span><span class="p">,</span><span class="n" style="color: #333;">nexons</span><span class="p">));</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4011" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4011
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<pre style="margin: 0;">+<span id="LC4011" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">exoni</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4012" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4012
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<pre style="margin: 0;">+<span id="LC4012" class="line" lang="c"> <span class="n" style="color: #333;">exonpos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">trstart</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4013" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4013
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<pre style="margin: 0;">+<span id="LC4013" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4014" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4014
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<pre style="margin: 0;">+<span id="LC4014" class="line" lang="c"> <span class="n" style="color: #333;">exonpos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">trstart</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">exonbounds</span><span class="p">[</span><span class="n" style="color: #333;">exoni</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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4015
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<pre style="margin: 0;">+<span id="LC4015" class="line" lang="c"> <span class="p">}</span></span>
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4016
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<pre style="margin: 0;">+<span id="LC4016" class="line" lang="c"> <span class="n" style="color: #333;">exon_residual</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">exonbounds</span><span class="p">[</span><span class="n" style="color: #333;">exoni</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">trstart</span><span class="p">;</span></span>
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4017
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<pre style="margin: 0;">+<span id="LC4017" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"exoni %d => exon_residual %d, exonpos %d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">exoni</span><span class="p">,</span><span class="n" style="color: #333;">exon_residual</span><span class="p">,</span><span class="n" style="color: #333;">exonpos</span><span class="p">));</span></span>
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4018
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<pre style="margin: 0;">+<span id="LC4018" class="line" lang="c"> </span>
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<td class="diff-line-num new new_line" data-linenumber="4019" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4019
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<pre style="margin: 0;">+<span id="LC4019" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Generate one substring per exon */</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4020" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4020
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<pre style="margin: 0;">+<span id="LC4020" class="line" lang="c"> <span class="n" style="color: #333;">genomicpos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">exonstarts</span><span class="p">[</span><span class="n" style="color: #333;">exoni</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">exonpos</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/* gminus */</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4021" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4021
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<pre style="margin: 0;">+<span id="LC4021" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"genomicpos %u = %u - %u</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">genomicpos</span><span class="p">,</span><span class="n" style="color: #333;">exonstarts</span><span class="p">[</span><span class="n" style="color: #333;">exoni</span><span class="p">],</span><span class="n" style="color: #333;">exonpos</span><span class="p">));</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4022" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4022
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<pre style="margin: 0;">+<span id="LC4022" class="line" lang="c"> <span class="n" style="color: #333;">align_residual</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">queryend</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">querystart</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4023" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4023
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<pre style="margin: 0;">+<span id="LC4023" class="line" lang="c"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">align_residual</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4024" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4024
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<pre style="margin: 0;">+<span id="LC4024" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"abortp %d, align_residual %d, exon_residual %d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">abortp</span><span class="p">,</span><span class="n" style="color: #333;">align_residual</span><span class="p">,</span><span class="n" style="color: #333;">exon_residual</span><span class="p">));</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4025" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4025
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<pre style="margin: 0;">+<span id="LC4025" class="line" lang="c"> <span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">align_residual</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">exon_residual</span><span class="p">)</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">align_residual</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">exon_residual</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4026" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4026
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<pre style="margin: 0;">+<span id="LC4026" class="line" lang="c"> <span class="n" style="color: #333;">queryend</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">querystart</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">len</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/* tplus */</span></span>
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3988
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<td class="diff-line-num new_line" data-linenumber="4027" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4027
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<pre style="margin: 0;"> <span id="LC4027" class="line" lang="c"> </span>
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3989
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<td class="diff-line-num new_line old" data-linenumber="4028" 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="LC3989" class="line" lang="c"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">exoni</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">nexons</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">exonbounds</span><span class="p">[</span><span class="n" style="color: #333;">exoni</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">trstart</span><span class="p">)</span> <span class="p">{</span></span>
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3990
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<pre style="margin: 0;">-<span id="LC3990" class="line" lang="c"> <span class="n" style="color: #333;">exoni</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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3991
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<pre style="margin: 0;">-<span id="LC3991" class="line" lang="c"> <span class="p">}</span></span>
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3992
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<pre style="margin: 0;">-<span id="LC3992" class="line" lang="c"></span>
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3993
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<td class="diff-line-num new_line old" data-linenumber="4028" 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="LC3993" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">exoni</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">nexons</span><span class="p">)</span> <span class="p">{</span></span>
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3994
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<td class="diff-line-num new_line old" data-linenumber="4028" 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="LC3994" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"ABORTING BECAUSE OF EXONI %d >= NEXONS %d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">exoni</span><span class="p">,</span><span class="n" style="color: #333;">nexons</span><span class="p">));</span></span>
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3995
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<pre style="margin: 0;">-<span id="LC3995" class="line" lang="c"> <span class="n" style="color: #333;">abortp</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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3996
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<pre style="margin: 0;">-<span id="LC3996" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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3997
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<td class="diff-line-num new_line old" data-linenumber="4028" 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="LC3997" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"(12) exoni %d out of nexons %d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">exoni</span><span class="p">,</span><span class="n" style="color: #333;">nexons</span><span class="p">));</span></span>
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3998
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<pre style="margin: 0;">-<span id="LC3998" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">exoni</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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3999
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<td class="diff-line-num new_line old" data-linenumber="4028" 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="LC3999" class="line" lang="c"> <span class="n" style="color: #333;">exonpos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">trstart</span><span class="p">;</span></span>
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4000
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<pre style="margin: 0;">-<span id="LC4000" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4001" 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">
4001
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<td class="diff-line-num new_line old" data-linenumber="4028" 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="LC4001" class="line" lang="c"> <span class="n" style="color: #333;">exonpos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">trstart</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">exonbounds</span><span class="p">[</span><span class="n" style="color: #333;">exoni</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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4002
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<td class="diff-line-num new_line old" data-linenumber="4028" 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="LC4002" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4003" 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">
4003
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<pre style="margin: 0;">-<span id="LC4003" class="line" lang="c"> <span class="n" style="color: #333;">exon_residual</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">exonbounds</span><span class="p">[</span><span class="n" style="color: #333;">exoni</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">trstart</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4004" 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">
4004
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<td class="diff-line-num new_line old" data-linenumber="4028" 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="LC4004" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"exoni %d => exon_residual %d, exonpos %d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">exoni</span><span class="p">,</span><span class="n" style="color: #333;">exon_residual</span><span class="p">,</span><span class="n" style="color: #333;">exonpos</span><span class="p">));</span></span>
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4005
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<td class="diff-line-num new_line old" data-linenumber="4028" 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="LC4005" class="line" lang="c"></span>
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<td class="diff-line-num old old_line" data-linenumber="4006" 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">
4006
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<td class="diff-line-num new_line old" data-linenumber="4028" 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="LC4006" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Generate one substring per exon */</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4007" 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">
4007
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<td class="diff-line-num new_line old" data-linenumber="4028" 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="LC4007" class="line" lang="c"> <span class="n" style="color: #333;">genomicpos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">exonstarts</span><span class="p">[</span><span class="n" style="color: #333;">exoni</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">exonpos</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/* gminus */</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4008" 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">
4008
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<td class="diff-line-num new_line old" data-linenumber="4028" 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="LC4008" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"genomicpos %u = %u - %u</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">genomicpos</span><span class="p">,</span><span class="n" style="color: #333;">exonstarts</span><span class="p">[</span><span class="n" style="color: #333;">exoni</span><span class="p">],</span><span class="n" style="color: #333;">exonpos</span><span class="p">));</span></span>
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4009
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<td class="diff-line-num new_line old" data-linenumber="4028" 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="LC4009" class="line" lang="c"> <span class="n" style="color: #333;">align_residual</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">queryend</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">querystart</span><span class="p">;</span></span>
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4010
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<td class="diff-line-num new_line old" data-linenumber="4028" 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="LC4010" class="line" lang="c"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">align_residual</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4011" 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">
4011
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<td class="diff-line-num new_line old" data-linenumber="4028" 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="LC4011" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"abortp %d, align_residual %d, exon_residual %d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">abortp</span><span class="p">,</span><span class="n" style="color: #333;">align_residual</span><span class="p">,</span><span class="n" style="color: #333;">exon_residual</span><span class="p">));</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4012" 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">
4012
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<td class="diff-line-num new_line old" data-linenumber="4028" 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="LC4012" class="line" lang="c"> <span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">align_residual</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">exon_residual</span><span class="p">)</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">align_residual</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">exon_residual</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4013" 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">
4013
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<td class="diff-line-num new_line old" data-linenumber="4028" 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="LC4013" class="line" lang="c"> <span class="n" style="color: #333;">queryend</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">querystart</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">len</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/* tplus */</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4014" 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">
4014
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<td class="diff-line-num new_line old" data-linenumber="4028" 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="LC4014" class="line" lang="c"></span>
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<td class="diff-line-num old old_line" data-linenumber="4015" 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">
4015
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<td class="diff-line-num new_line old" data-linenumber="4028" 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="LC4015" class="line" lang="c"> <span class="n" style="color: #333;">alignstart</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">chroffset</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">genomicpos</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4016" 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">
4016
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<pre style="margin: 0;">-<span id="LC4016" class="line" lang="c"> <span class="n" style="color: #333;">alignend</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alignstart</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">len</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/* gminus */</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4017" 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">
4017
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<td class="diff-line-num new_line old" data-linenumber="4028" 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="LC4017" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">left</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alignend</span> <span class="o" style="font-weight: 600;">-</span> <span class="p">(</span><span class="n" style="color: #333;">querylength</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">queryend</span><span class="p">));</span> <span class="cm" style="color: #998; font-style: italic;">/* tplus != gminus */</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4018" 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">
4018
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<td class="diff-line-num new_line old" data-linenumber="4028" 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="LC4018" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"tr ultrfast gap case 2 2nd part query %d..%d, align %u..%u [%u..%u], left %u = %u - (%d - %d)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4019" 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">
4019
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<td class="diff-line-num new_line old" data-linenumber="4028" 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="LC4019" class="line" lang="c"> <span class="n" style="color: #333;">querystart</span><span class="p">,</span><span class="n" style="color: #333;">queryend</span><span class="p">,</span><span class="n" style="color: #333;">alignstart</span><span class="p">,</span><span class="n" style="color: #333;">alignend</span><span class="p">,</span><span class="n" style="color: #333;">alignstart</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">chroffset</span><span class="p">,</span><span class="n" style="color: #333;">alignend</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">chroffset</span><span class="p">,</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4020" 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">
4020
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<td class="diff-line-num new_line old" data-linenumber="4028" 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="LC4020" class="line" lang="c"> <span class="n" style="color: #333;">left</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">chroffset</span><span class="p">,</span><span class="n" style="color: #333;">alignend</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">chroffset</span><span class="p">,</span><span class="n" style="color: #333;">querylength</span><span class="p">,</span><span class="n" style="color: #333;">queryend</span><span class="p">));</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4021" 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">
4021
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<td class="diff-line-num new_line old" data-linenumber="4028" 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="LC4021" class="line" lang="c"></span>
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<td class="diff-line-num old old_line" data-linenumber="4022" 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">
4022
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<td class="diff-line-num new_line old" data-linenumber="4028" 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="LC4022" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* tplus: push alignstart first */</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4023" 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">
4023
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<td class="diff-line-num new_line old" data-linenumber="4028" 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="LC4023" class="line" lang="c"> <span class="n" style="color: #333;">endpoints</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Uintlist_push</span><span class="p">(</span><span class="n" style="color: #333;">endpoints</span><span class="p">,(</span><span class="n" style="color: #333;">Chrpos_T</span><span class="p">)</span> <span class="p">(</span><span class="n" style="color: #333;">alignstart</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">chroffset</span><span class="p">));</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4024" 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">
4024
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<td class="diff-line-num new_line old" data-linenumber="4028" 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="LC4024" class="line" lang="c"> <span class="n" style="color: #333;">endpoints</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Uintlist_push</span><span class="p">(</span><span class="n" style="color: #333;">endpoints</span><span class="p">,(</span><span class="n" style="color: #333;">Chrpos_T</span><span class="p">)</span> <span class="p">(</span><span class="n" style="color: #333;">alignend</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">chroffset</span><span class="p">));</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4025" 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">
4025
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<td class="diff-line-num new_line old" data-linenumber="4028" 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="LC4025" class="line" lang="c"></span>
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<td class="diff-line-num old old_line" data-linenumber="4026" 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">
4026
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<td class="diff-line-num new_line old" data-linenumber="4028" 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="LC4026" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">align_residual</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">exon_residual</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4027" 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">
4027
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<td class="diff-line-num new_line old" data-linenumber="4028" 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="LC4027" class="line" lang="c"> <span class="n" style="color: #333;">exon_residual</span> <span class="o" style="font-weight: 600;">-=</span> <span class="n" style="color: #333;">align_residual</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/* Need to know this if we have a following deletion */</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4028" 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">
4028
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<td class="diff-line-num new_line old" data-linenumber="4028" 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="LC4028" class="line" lang="c"> <span class="n" style="color: #333;">align_residual</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4029" 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">
4029
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<td class="diff-line-num new_line old" data-linenumber="4028" 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="LC4029" class="line" lang="c"> <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="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">exoni</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">nexons</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4030" 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">
4030
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<td class="diff-line-num new_line old" data-linenumber="4028" 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="LC4030" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Aligning past the end of the transcript */</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4031" 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">
4031
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<td class="diff-line-num new_line old" data-linenumber="4028" 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="LC4031" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"4 ABORTING BECAUSE ALIGNING PAST END OF TRANSCRIPT</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">));</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="4032" 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">
4032
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<td class="diff-line-num new_line old" data-linenumber="4028" 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="LC4032" class="line" lang="c"> <span class="n" style="color: #333;">align_residual</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="4033" 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">
4033
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<td class="diff-line-num new_line old" data-linenumber="4028" 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="LC4033" class="line" lang="c"> <span class="n" style="color: #333;">abortp</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="4034" 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">
4034
</td>
<td class="diff-line-num new_line old" data-linenumber="4028" 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="LC4034" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4035" 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">
4035
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<td class="diff-line-num new_line old" data-linenumber="4028" 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="LC4035" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* nintrons += 1; */</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4036" 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">
4036
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<pre style="margin: 0;">-<span id="LC4036" class="line" lang="c"> <span class="n" style="color: #333;">align_residual</span> <span class="o" style="font-weight: 600;">-=</span> <span class="n" style="color: #333;">len</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4037" 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">
4037
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<td class="diff-line-num new_line old" data-linenumber="4028" 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="LC4037" class="line" lang="c"> <span class="n" style="color: #333;">querystart</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">len</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/* tplus */</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4038" 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">
4038
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<td class="diff-line-num new_line old" data-linenumber="4028" 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="LC4038" class="line" lang="c"> <span class="n" style="color: #333;">genomicpos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">exonstarts</span><span class="p">[</span><span class="n" style="color: #333;">exoni</span><span class="p">];</span> <span class="cm" style="color: #998; font-style: italic;">/* gminus */</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4039" 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">
4039
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<td class="diff-line-num new_line old" data-linenumber="4028" 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="LC4039" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"genomicpos %u = %u</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">genomicpos</span><span class="p">,</span><span class="n" style="color: #333;">exonstarts</span><span class="p">[</span><span class="n" style="color: #333;">exoni</span><span class="p">]));</span></span>
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4040
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<td class="diff-line-num new_line old" data-linenumber="4028" 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="LC4040" class="line" lang="c"> <span class="n" style="color: #333;">exon_residual</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">exonbounds</span><span class="p">[</span><span class="n" style="color: #333;">exoni</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">exonbounds</span><span class="p">[</span><span class="n" style="color: #333;">exoni</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 old old_line" data-linenumber="4041" 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">
4041
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<td class="diff-line-num new_line old" data-linenumber="4028" 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="LC4041" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"INTRON</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">));</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4042" 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">
4042
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<td class="diff-line-num new_line old" data-linenumber="4028" 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="LC4042" class="line" lang="c"> <span class="n" style="color: #333;">gaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Intlist_push</span><span class="p">(</span><span class="n" style="color: #333;">gaps</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4043" 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">
4043
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<td class="diff-line-num new_line old" data-linenumber="4028" 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="LC4043" class="line" lang="c"> <span class="p">}</span></span>
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4044
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<td class="diff-line-num new_line old" data-linenumber="4028" 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="LC4044" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4045" 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">
4045
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<td class="diff-line-num new_line old" data-linenumber="4028" 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="LC4045" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num new old_line" data-linenumber="4046" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="4028" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4028
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<pre style="margin: 0;">+<span id="LC4028" class="line" lang="c"> <span class="n" style="color: #333;">alignstart</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">chroffset</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">genomicpos</span><span class="p">;</span></span>
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<td class="diff-line-num new old_line" data-linenumber="4046" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="4029" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4029
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<pre style="margin: 0;">+<span id="LC4029" class="line" lang="c"> <span class="n" style="color: #333;">alignend</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alignstart</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">len</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/* gminus */</span></span>
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<td class="diff-line-num new old_line" data-linenumber="4046" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="4030" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4030
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<pre style="margin: 0;">+<span id="LC4030" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">left</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alignend</span> <span class="o" style="font-weight: 600;">-</span> <span class="p">(</span><span class="n" style="color: #333;">querylength</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">queryend</span><span class="p">));</span> <span class="cm" style="color: #998; font-style: italic;">/* tplus != gminus */</span></span>
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<td class="diff-line-num new old_line" data-linenumber="4046" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="4031" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4031
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<pre style="margin: 0;">+<span id="LC4031" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"tr ultrfast gap case 2 2nd part query %d..%d, align %u..%u [%u..%u], left %u = %u - (%d - %d)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span></span>
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<td class="diff-line-num new old_line" data-linenumber="4046" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="4032" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4032
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<pre style="margin: 0;">+<span id="LC4032" class="line" lang="c"> <span class="n" style="color: #333;">querystart</span><span class="p">,</span><span class="n" style="color: #333;">queryend</span><span class="p">,</span><span class="n" style="color: #333;">alignstart</span><span class="p">,</span><span class="n" style="color: #333;">alignend</span><span class="p">,</span><span class="n" style="color: #333;">alignstart</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">chroffset</span><span class="p">,</span><span class="n" style="color: #333;">alignend</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">chroffset</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4033" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4033
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<pre style="margin: 0;">+<span id="LC4033" class="line" lang="c"> <span class="n" style="color: #333;">left</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">chroffset</span><span class="p">,</span><span class="n" style="color: #333;">alignend</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">chroffset</span><span class="p">,</span><span class="n" style="color: #333;">querylength</span><span class="p">,</span><span class="n" style="color: #333;">queryend</span><span class="p">));</span></span>
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4046
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<td class="diff-line-num new_line" data-linenumber="4034" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4034
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<pre style="margin: 0;"> <span id="LC4034" class="line" lang="c"> </span>
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<td class="diff-line-num old old_line" data-linenumber="4047" 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">
4047
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<td class="diff-line-num new_line old" data-linenumber="4035" 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="LC4047" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">abortp</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4048" 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">
4048
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<td class="diff-line-num new_line old" data-linenumber="4035" 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="LC4048" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"ABORTING PATH</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">));</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4049" 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">
4049
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<td class="diff-line-num new_line old" data-linenumber="4035" 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="LC4049" class="line" lang="c"> <span class="n" style="color: #333;">Uintlist_free</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">endpoints</span><span class="p">);</span></span>
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4050
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<pre style="margin: 0;">-<span id="LC4050" class="line" lang="c"> <span class="n" style="color: #333;">Intlist_free</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">gaps</span><span class="p">);</span></span>
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4035
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<pre style="margin: 0;">+<span id="LC4035" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* tplus: push alignstart first */</span></span>
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4036
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<pre style="margin: 0;">+<span id="LC4036" class="line" lang="c"> <span class="n" style="color: #333;">endpoints</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Uintlist_push</span><span class="p">(</span><span class="n" style="color: #333;">endpoints</span><span class="p">,(</span><span class="n" style="color: #333;">Chrpos_T</span><span class="p">)</span> <span class="p">(</span><span class="n" style="color: #333;">alignstart</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">chroffset</span><span class="p">));</span></span>
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4037
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<pre style="margin: 0;">+<span id="LC4037" class="line" lang="c"> <span class="n" style="color: #333;">endpoints</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Uintlist_push</span><span class="p">(</span><span class="n" style="color: #333;">endpoints</span><span class="p">,(</span><span class="n" style="color: #333;">Chrpos_T</span><span class="p">)</span> <span class="p">(</span><span class="n" style="color: #333;">alignend</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">chroffset</span><span class="p">));</span></span>
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4038
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<pre style="margin: 0;">+<span id="LC4038" class="line" lang="c"> </span>
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4039
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<pre style="margin: 0;">+<span id="LC4039" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">align_residual</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">exon_residual</span><span class="p">)</span> <span class="p">{</span></span>
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4040
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<pre style="margin: 0;">+<span id="LC4040" class="line" lang="c"> <span class="n" style="color: #333;">exon_residual</span> <span class="o" style="font-weight: 600;">-=</span> <span class="n" style="color: #333;">align_residual</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/* Need to know this if we have a following deletion */</span></span>
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4041
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<pre style="margin: 0;">+<span id="LC4041" class="line" lang="c"> <span class="n" style="color: #333;">align_residual</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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4042
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<pre style="margin: 0;">+<span id="LC4042" class="line" lang="c"> <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="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">exoni</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">nexons</span><span class="p">)</span> <span class="p">{</span></span>
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4043
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<pre style="margin: 0;">+<span id="LC4043" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Aligning past the end of the transcript */</span></span>
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4044
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<pre style="margin: 0;">+<span id="LC4044" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"4 ABORTING BECAUSE ALIGNING PAST END OF TRANSCRIPT</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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4045
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<pre style="margin: 0;">+<span id="LC4045" class="line" lang="c"> <span class="n" style="color: #333;">align_residual</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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4046
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<pre style="margin: 0;">+<span id="LC4046" class="line" lang="c"> <span class="n" style="color: #333;">abortp</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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4051
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4047
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<pre style="margin: 0;"> <span id="LC4047" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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4052
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<td class="diff-line-num new_line old" data-linenumber="4048" 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="LC4052" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* gminus: Do not reverse endpoints or gaps */</span></span>
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4053
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<pre style="margin: 0;">-<span id="LC4053" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"MINUS PATH %d. ENDPOINTS: %s. GAPS: %s</span><span class="se" style="color: #d14;">\n\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span></span>
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4054
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<pre style="margin: 0;">-<span id="LC4054" class="line" lang="c"> <span class="n" style="color: #333;">ngminus</span><span class="p">,</span><span class="n" style="color: #333;">Uintlist_to_string</span><span class="p">(</span><span class="n" style="color: #333;">endpoints</span><span class="p">),</span><span class="n" style="color: #333;">Intlist_to_string</span><span class="p">(</span><span class="n" style="color: #333;">gaps</span><span class="p">)));</span></span>
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4055
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<pre style="margin: 0;">-<span id="LC4055" class="line" lang="c"> <span class="n" style="color: #333;">gminus_paths</span><span class="p">[</span><span class="n" style="color: #333;">ngminus</span><span class="o" style="font-weight: 600;">++</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Path_new</span><span class="p">(</span><span class="n" style="color: #333;">total_nmatches</span><span class="p">,</span><span class="n" style="color: #333;">trnum</span><span class="p">,</span><span class="n" style="color: #333;">overall_trstart</span><span class="p">,</span><span class="n" style="color: #333;">overall_trend</span><span class="p">,</span></span>
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4056
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<pre style="margin: 0;">-<span id="LC4056" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/*trim_low*/</span><span class="n" style="color: #333;">trim3</span><span class="p">,</span><span class="cm" style="color: #998; font-style: italic;">/*trim_high*/</span><span class="n" style="color: #333;">trim5</span><span class="p">,</span></span>
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4057
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<pre style="margin: 0;">-<span id="LC4057" class="line" lang="c"> <span class="n" style="color: #333;">chrnum</span><span class="p">,</span><span class="n" style="color: #333;">chroffset</span><span class="p">,</span><span class="n" style="color: #333;">chrhigh</span><span class="p">,</span><span class="n" style="color: #333;">chrlength</span><span class="p">,</span><span class="n" style="color: #333;">endpoints</span><span class="p">,</span><span class="n" style="color: #333;">gaps</span><span class="p">,</span><span class="n" style="color: #333;">concordantp</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4048" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4048
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<pre style="margin: 0;">+<span id="LC4048" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* nintrons += 1; */</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4049" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4049
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<pre style="margin: 0;">+<span id="LC4049" class="line" lang="c"> <span class="n" style="color: #333;">align_residual</span> <span class="o" style="font-weight: 600;">-=</span> <span class="n" style="color: #333;">len</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4050" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4050
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<pre style="margin: 0;">+<span id="LC4050" class="line" lang="c"> <span class="n" style="color: #333;">querystart</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">len</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/* tplus */</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4051" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4051
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<pre style="margin: 0;">+<span id="LC4051" class="line" lang="c"> <span class="n" style="color: #333;">genomicpos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">exonstarts</span><span class="p">[</span><span class="n" style="color: #333;">exoni</span><span class="p">];</span> <span class="cm" style="color: #998; font-style: italic;">/* gminus */</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4052" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4052
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<pre style="margin: 0;">+<span id="LC4052" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"genomicpos %u = %u</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">genomicpos</span><span class="p">,</span><span class="n" style="color: #333;">exonstarts</span><span class="p">[</span><span class="n" style="color: #333;">exoni</span><span class="p">]));</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4053" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4053
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<pre style="margin: 0;">+<span id="LC4053" class="line" lang="c"> <span class="n" style="color: #333;">exon_residual</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">exonbounds</span><span class="p">[</span><span class="n" style="color: #333;">exoni</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">exonbounds</span><span class="p">[</span><span class="n" style="color: #333;">exoni</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">];</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4054" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4054
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<pre style="margin: 0;">+<span id="LC4054" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"INTRON</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">));</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4055" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4055
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<pre style="margin: 0;">+<span id="LC4055" class="line" lang="c"> <span class="n" style="color: #333;">gaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Intlist_push</span><span class="p">(</span><span class="n" style="color: #333;">gaps</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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4058
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4056
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<pre style="margin: 0;"> <span id="LC4056" class="line" lang="c"> <span class="p">}</span></span>
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4059
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4057
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<pre style="margin: 0;"> <span id="LC4057" class="line" lang="c"> <span class="p">}</span></span>
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4060
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4058
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<pre style="margin: 0;"> <span id="LC4058" class="line" lang="c"> <span class="p">}</span></span>
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4059
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<pre style="margin: 0;">+<span id="LC4059" class="line" lang="c"> </span>
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4060
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<pre style="margin: 0;">+<span id="LC4060" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">abortp</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">)</span> <span class="p">{</span></span>
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4061
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<pre style="margin: 0;">+<span id="LC4061" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"ABORTING PATH</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">));</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4062" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4062
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<pre style="margin: 0;">+<span id="LC4062" class="line" lang="c"> <span class="n" style="color: #333;">Uintlist_free</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">endpoints</span><span class="p">);</span></span>
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4063
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<pre style="margin: 0;">+<span id="LC4063" class="line" lang="c"> <span class="n" style="color: #333;">Intlist_free</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">gaps</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4064" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4064
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<pre style="margin: 0;">+<span id="LC4064" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4065" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4065
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<pre style="margin: 0;">+<span id="LC4065" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* gminus: Do not reverse endpoints or gaps */</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4066" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4066
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<pre style="margin: 0;">+<span id="LC4066" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"MINUS PATH %d. ENDPOINTS: %s. GAPS: %s</span><span class="se" style="color: #d14;">\n\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4067" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4067
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<pre style="margin: 0;">+<span id="LC4067" class="line" lang="c"> <span class="n" style="color: #333;">ngminus</span><span class="p">,</span><span class="n" style="color: #333;">Uintlist_to_string</span><span class="p">(</span><span class="n" style="color: #333;">endpoints</span><span class="p">),</span><span class="n" style="color: #333;">Intlist_to_string</span><span class="p">(</span><span class="n" style="color: #333;">gaps</span><span class="p">)));</span></span>
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4068
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<pre style="margin: 0;">+<span id="LC4068" class="line" lang="c"> <span class="n" style="color: #333;">gminus_paths</span><span class="p">[</span><span class="n" style="color: #333;">ngminus</span><span class="o" style="font-weight: 600;">++</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Path_new</span><span class="p">(</span><span class="n" style="color: #333;">total_nmatches</span><span class="p">,</span><span class="n" style="color: #333;">trnum</span><span class="p">,</span><span class="n" style="color: #333;">overall_trstart</span><span class="p">,</span><span class="n" style="color: #333;">overall_trend</span><span class="p">,</span></span>
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4069
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<pre style="margin: 0;">+<span id="LC4069" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/*trim_low*/</span><span class="n" style="color: #333;">trim3</span><span class="p">,</span><span class="cm" style="color: #998; font-style: italic;">/*trim_high*/</span><span class="n" style="color: #333;">trim5</span><span class="p">,</span></span>
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4070
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<pre style="margin: 0;">+<span id="LC4070" class="line" lang="c"> <span class="n" style="color: #333;">chrnum</span><span class="p">,</span><span class="n" style="color: #333;">chroffset</span><span class="p">,</span><span class="n" style="color: #333;">chrhigh</span><span class="p">,</span><span class="n" style="color: #333;">chrlength</span><span class="p">,</span><span class="n" style="color: #333;">endpoints</span><span class="p">,</span><span class="n" style="color: #333;">gaps</span><span class="p">,</span><span class="n" style="color: #333;">concordantp</span><span class="p">);</span></span>
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4071
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<pre style="margin: 0;">+<span id="LC4071" class="line" lang="c"> <span class="p">}</span></span>
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4061
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4072
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<pre style="margin: 0;"> <span id="LC4072" class="line" lang="c"> <span class="p">}</span></span>
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4062
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4073
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<pre style="margin: 0;"> <span id="LC4073" class="line" lang="c"> <span class="p">}</span></span>
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4063
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4074
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<pre style="margin: 0;"> <span id="LC4074" class="line" lang="c"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4108" style="width: 35px; color: rgba(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="4119" style="width: 35px; color: rgba(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">@@ -4108,475 +4119,479 @@ search_transcriptome_ends (Path_T **tplus_gplus_paths, int *n_tplus_gplus,</td>
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4108
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4119
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<pre style="margin: 0;"> <span id="LC4119" class="line" lang="c"> <span class="n" style="color: #333;">adj</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="p">(</span><span class="n" style="color: #333;">tr_univdiagonala</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">tr_univdiagonalb</span><span class="p">);</span></span>
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4109
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4120
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<pre style="margin: 0;"> <span id="LC4120" class="line" lang="c"> <span class="n" style="color: #333;">debug2a</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"Setting b first, a second, adj %d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">adj</span><span class="p">));</span></span>
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4110
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4121
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<pre style="margin: 0;"> <span id="LC4121" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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4122
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<pre style="margin: 0;">+<span id="LC4122" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Read does not extend to the ends, so this method is not applicable */</span></span>
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4111
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4123
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<pre style="margin: 0;"> <span id="LC4123" class="line" lang="c"> <span class="n" style="color: #333;">adj</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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4112
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4124
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<pre style="margin: 0;"> <span id="LC4124" class="line" lang="c"> <span class="p">}</span></span>
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4113
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4125
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<pre style="margin: 0;"> <span id="LC4125" class="line" lang="c"></span>
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4114
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<pre style="margin: 0;">-<span id="LC4114" class="line" lang="c"> <span class="n" style="color: #333;">abortp</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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4115
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<td class="diff-line-num new_line old" data-linenumber="4126" 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="LC4115" class="line" lang="c"> <span class="n" style="color: #333;">trnum</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Univ_IIT_get_trnum</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">troffset</span><span class="p">,</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">trhigh</span><span class="p">,</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">trlength</span><span class="p">,</span><span class="n" style="color: #333;">transcript_iit</span><span class="p">,</span><span class="cm" style="color: #998; font-style: italic;">/*low*/</span><span class="n" style="color: #333;">low0</span><span class="p">,</span><span class="cm" style="color: #998; font-style: italic;">/*high*/</span><span class="n" style="color: #333;">high0</span><span class="p">);</span></span>
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4116
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<pre style="margin: 0;">-<span id="LC4116" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"trnum is %d: %s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">trnum</span><span class="p">,</span><span class="n" style="color: #333;">Univ_IIT_label</span><span class="p">(</span><span class="n" style="color: #333;">transcript_iit</span><span class="p">,</span><span class="n" style="color: #333;">trnum</span><span class="p">,</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">allocp</span><span class="p">)));</span></span>
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4117
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<pre style="margin: 0;">-<span id="LC4117" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">chrnum</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Transcriptome_chrnum</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">transcript_genestrand</span><span class="p">,</span><span class="n" style="color: #333;">transcriptome</span><span class="p">,</span><span class="n" style="color: #333;">trnum</span><span class="p">))</span> <span class="o" style="font-weight: 600;"><=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4118" 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">
4118
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<pre style="margin: 0;">-<span id="LC4118" class="line" lang="c"> <span class="n" style="color: #333;">abortp</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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4119
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<pre style="margin: 0;">-<span id="LC4119" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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4120
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<pre style="margin: 0;">-<span id="LC4120" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">transcript_genestrand</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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4121
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<pre style="margin: 0;">-<span id="LC4121" class="line" lang="c"> <span class="n" style="color: #333;">want_lowest_coordinate_p</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4122" 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">
4122
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<td class="diff-line-num new_line old" data-linenumber="4126" 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="LC4122" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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4123
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<td class="diff-line-num new_line old" data-linenumber="4126" 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="LC4123" class="line" lang="c"> <span class="n" style="color: #333;">want_lowest_coordinate_p</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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4124
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<td class="diff-line-num new_line old" data-linenumber="4126" 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="LC4124" class="line" lang="c"> <span class="p">}</span></span>
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4125
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<td class="diff-line-num new_line old" data-linenumber="4126" 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="LC4125" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"trnum %d, transcript_genestrand %d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">trnum</span><span class="p">,</span><span class="n" style="color: #333;">transcript_genestrand</span><span class="p">));</span></span>
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4126
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<pre style="margin: 0;">-<span id="LC4126" class="line" lang="c"></span>
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4127
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<td class="diff-line-num new_line old" data-linenumber="4126" 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="LC4127" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">adj</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>
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<td class="diff-line-num old old_line" data-linenumber="4128" 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">
4128
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<td class="diff-line-num new_line old" data-linenumber="4126" 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="LC4128" class="line" lang="c"> <span class="p">(</span><span class="n" style="color: #333;">indel_pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Indel_resolve_middle_deletion</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">best_nmismatches_i</span><span class="p">,</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">best_nmismatches_j</span><span class="p">,</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4129" 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">
4129
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<pre style="margin: 0;">-<span id="LC4129" class="line" lang="c"> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">best_ref_nmismatches_i</span><span class="p">,</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">best_ref_nmismatches_j</span><span class="p">,</span></span>
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4130
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<td class="diff-line-num new_line old" data-linenumber="4126" 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="LC4130" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/*left*/</span><span class="n" style="color: #333;">tr_left0</span><span class="p">,</span><span class="cm" style="color: #998; font-style: italic;">/*indels*/</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">adj</span><span class="p">,</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4131" 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">
4131
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<td class="diff-line-num new_line old" data-linenumber="4126" 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="LC4131" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/*mismatch_positions_left*/</span><span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span><span class="cm" style="color: #998; font-style: italic;">/*nmismatches_left*/</span><span class="mi" style="color: #099;">0</span><span class="p">,</span></span>
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4132
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<td class="diff-line-num new_line old" data-linenumber="4126" 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="LC4132" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/*mismatch_positions_right*/</span><span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span><span class="cm" style="color: #998; font-style: italic;">/*nmismatches_right*/</span><span class="mi" style="color: #099;">0</span><span class="p">,</span></span>
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4133
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<td class="diff-line-num new_line old" data-linenumber="4126" 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="LC4133" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/*ome*/</span><span class="n" style="color: #333;">transcriptomebits</span><span class="p">,</span><span class="cm" style="color: #998; font-style: italic;">/*ome_alt*/</span><span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span><span class="n" style="color: #333;">query_compress_rev</span><span class="p">,</span></span>
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4134
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<td class="diff-line-num new_line old" data-linenumber="4126" 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="LC4134" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/*querystart*/</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="cm" style="color: #998; font-style: italic;">/*queryend*/</span><span class="n" style="color: #333;">querylength</span><span class="p">,</span><span class="n" style="color: #333;">querylength</span><span class="p">,</span></span>
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4135
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<td class="diff-line-num new_line old" data-linenumber="4126" 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="LC4135" class="line" lang="c"> <span class="n" style="color: #333;">nmismatches_allowed</span><span class="p">,</span><span class="cm" style="color: #998; font-style: italic;">/*plusp*/</span><span class="nb" style="color: #0086b3;">false</span><span class="p">,</span><span class="cm" style="color: #998; font-style: italic;">/*genestrand*/</span><span class="mi" style="color: #099;">0</span><span class="p">,</span></span>
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4136
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<pre style="margin: 0;">-<span id="LC4136" class="line" lang="c"> <span class="n" style="color: #333;">want_lowest_coordinate_p</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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4137
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<pre style="margin: 0;">-<span id="LC4137" class="line" lang="c"> <span class="n" style="color: #333;">ninserts</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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4138
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<td class="diff-line-num new_line old" data-linenumber="4126" 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="LC4138" class="line" lang="c"> <span class="n" style="color: #333;">nindels</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">adj</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4139" 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">
4139
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<pre style="margin: 0;">-<span id="LC4139" class="line" lang="c"> <span class="n" style="color: #333;">total_nmatches</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">querylength</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">best_nmismatches_i</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">best_nmismatches_j</span><span class="p">;</span></span>
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4140
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<pre style="margin: 0;">-<span id="LC4140" class="line" lang="c"> <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;">adj</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>
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<td class="diff-line-num old old_line" data-linenumber="4141" 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">
4141
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<td class="diff-line-num new_line old" data-linenumber="4126" 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="LC4141" class="line" lang="c"> <span class="p">(</span><span class="n" style="color: #333;">indel_pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Indel_resolve_middle_insertion</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">best_nmismatches_i</span><span class="p">,</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">best_nmismatches_j</span><span class="p">,</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4142" 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">
4142
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<pre style="margin: 0;">-<span id="LC4142" class="line" lang="c"> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">best_ref_nmismatches_i</span><span class="p">,</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">best_ref_nmismatches_j</span><span class="p">,</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4143" 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">
4143
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<td class="diff-line-num new_line old" data-linenumber="4126" 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="LC4143" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/*left*/</span><span class="n" style="color: #333;">tr_left0</span><span class="p">,</span><span class="cm" style="color: #998; font-style: italic;">/*indels*/</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">adj</span><span class="p">,</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4144" 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">
4144
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<td class="diff-line-num new_line old" data-linenumber="4126" 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="LC4144" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/*mismatch_positions_left*/</span><span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span><span class="cm" style="color: #998; font-style: italic;">/*nmismatches_left*/</span><span class="mi" style="color: #099;">0</span><span class="p">,</span></span>
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4145
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<td class="diff-line-num new_line old" data-linenumber="4126" 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="LC4145" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/*mismatch_positions_right*/</span><span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span><span class="cm" style="color: #998; font-style: italic;">/*nmismatches_right*/</span><span class="mi" style="color: #099;">0</span><span class="p">,</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4146" 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">
4146
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<td class="diff-line-num new_line old" data-linenumber="4126" 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="LC4146" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/*ome*/</span><span class="n" style="color: #333;">transcriptomebits</span><span class="p">,</span><span class="cm" style="color: #998; font-style: italic;">/*ome_alt*/</span><span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span><span class="n" style="color: #333;">query_compress_rev</span><span class="p">,</span></span>
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4147
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<td class="diff-line-num new_line old" data-linenumber="4126" 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="LC4147" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/*querystart*/</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="cm" style="color: #998; font-style: italic;">/*queryend*/</span><span class="n" style="color: #333;">querylength</span><span class="p">,</span><span class="n" style="color: #333;">querylength</span><span class="p">,</span></span>
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4148
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<td class="diff-line-num new_line old" data-linenumber="4126" 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="LC4148" class="line" lang="c"> <span class="n" style="color: #333;">nmismatches_allowed</span><span class="p">,</span><span class="cm" style="color: #998; font-style: italic;">/*plusp*/</span><span class="nb" style="color: #0086b3;">false</span><span class="p">,</span><span class="cm" style="color: #998; font-style: italic;">/*genestrand*/</span><span class="mi" style="color: #099;">0</span><span class="p">,</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4149" 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">
4149
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<pre style="margin: 0;">-<span id="LC4149" class="line" lang="c"> <span class="n" style="color: #333;">want_lowest_coordinate_p</span><span class="p">))</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4150" 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">
4150
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<td class="diff-line-num new_line old" data-linenumber="4126" 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="LC4150" class="line" lang="c"> <span class="n" style="color: #333;">ninserts</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nindels</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">adj</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4151" 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">
4151
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<td class="diff-line-num new_line old" data-linenumber="4126" 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="LC4151" class="line" lang="c"> <span class="n" style="color: #333;">total_nmatches</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">querylength</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">best_nmismatches_i</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">best_nmismatches_j</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">ninserts</span><span class="p">;</span></span>
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4152
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<td class="diff-line-num new_line old" data-linenumber="4126" 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="LC4152" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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4126
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<pre style="margin: 0;">+<span id="LC4126" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">adj</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4127
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<pre style="margin: 0;">+<span id="LC4127" class="line" lang="c"> <span class="n" style="color: #333;">trnum</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Univ_IIT_get_trnum</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">troffset</span><span class="p">,</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">trhigh</span><span class="p">,</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">trlength</span><span class="p">,</span><span class="n" style="color: #333;">transcript_iit</span><span class="p">,</span><span class="cm" style="color: #998; font-style: italic;">/*low*/</span><span class="n" style="color: #333;">low0</span><span class="p">,</span><span class="cm" style="color: #998; font-style: italic;">/*high*/</span><span class="n" style="color: #333;">high0</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4128
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<pre style="margin: 0;">+<span id="LC4128" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"trnum is %d: %s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">trnum</span><span class="p">,</span><span class="n" style="color: #333;">Univ_IIT_label</span><span class="p">(</span><span class="n" style="color: #333;">transcript_iit</span><span class="p">,</span><span class="n" style="color: #333;">trnum</span><span class="p">,</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">allocp</span><span class="p">)));</span></span>
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4129
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<pre style="margin: 0;">+<span id="LC4129" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">chrnum</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Transcriptome_chrnum</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">transcript_genestrand</span><span class="p">,</span><span class="n" style="color: #333;">transcriptome</span><span class="p">,</span><span class="n" style="color: #333;">trnum</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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4153
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4130
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<pre style="margin: 0;"> <span id="LC4130" class="line" lang="c"> <span class="n" style="color: #333;">adj</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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4131
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<pre style="margin: 0;">+<span id="LC4131" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4132
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<pre style="margin: 0;">+<span id="LC4132" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">transcript_genestrand</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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4133
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<pre style="margin: 0;">+<span id="LC4133" class="line" lang="c"> <span class="n" style="color: #333;">want_lowest_coordinate_p</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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4134
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<pre style="margin: 0;">+<span id="LC4134" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4135" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4135
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<pre style="margin: 0;">+<span id="LC4135" class="line" lang="c"> <span class="n" style="color: #333;">want_lowest_coordinate_p</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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4136
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<pre style="margin: 0;">+<span id="LC4136" class="line" lang="c"> <span class="p">}</span></span>
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4137
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<pre style="margin: 0;">+<span id="LC4137" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"trnum %d, transcript_genestrand %d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">trnum</span><span class="p">,</span><span class="n" style="color: #333;">transcript_genestrand</span><span class="p">));</span></span>
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4138
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<pre style="margin: 0;">+<span id="LC4138" class="line" lang="c"> </span>
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<td class="diff-line-num new new_line" data-linenumber="4139" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4139
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<pre style="margin: 0;">+<span id="LC4139" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">adj</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>
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4140
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<pre style="margin: 0;">+<span id="LC4140" class="line" lang="c"> <span class="p">(</span><span class="n" style="color: #333;">indel_pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Indel_resolve_middle_deletion</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">best_nmismatches_i</span><span class="p">,</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">best_nmismatches_j</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4141
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<pre style="margin: 0;">+<span id="LC4141" class="line" lang="c"> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">best_ref_nmismatches_i</span><span class="p">,</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">best_ref_nmismatches_j</span><span class="p">,</span></span>
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4142
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<pre style="margin: 0;">+<span id="LC4142" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/*left*/</span><span class="n" style="color: #333;">tr_left0</span><span class="p">,</span><span class="cm" style="color: #998; font-style: italic;">/*indels*/</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">adj</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4143
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<pre style="margin: 0;">+<span id="LC4143" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/*mismatch_positions_left*/</span><span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span><span class="cm" style="color: #998; font-style: italic;">/*nmismatches_left*/</span><span class="mi" style="color: #099;">0</span><span class="p">,</span></span>
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4144
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<pre style="margin: 0;">+<span id="LC4144" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/*mismatch_positions_right*/</span><span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span><span class="cm" style="color: #998; font-style: italic;">/*nmismatches_right*/</span><span class="mi" style="color: #099;">0</span><span class="p">,</span></span>
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4145
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<pre style="margin: 0;">+<span id="LC4145" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/*ome*/</span><span class="n" style="color: #333;">transcriptomebits</span><span class="p">,</span><span class="cm" style="color: #998; font-style: italic;">/*ome_alt*/</span><span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span><span class="n" style="color: #333;">query_compress_rev</span><span class="p">,</span></span>
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4146
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<pre style="margin: 0;">+<span id="LC4146" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/*querystart*/</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="cm" style="color: #998; font-style: italic;">/*queryend*/</span><span class="n" style="color: #333;">querylength</span><span class="p">,</span><span class="n" style="color: #333;">querylength</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4147" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4147
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<pre style="margin: 0;">+<span id="LC4147" class="line" lang="c"> <span class="n" style="color: #333;">nmismatches_allowed</span><span class="p">,</span><span class="cm" style="color: #998; font-style: italic;">/*plusp*/</span><span class="nb" style="color: #0086b3;">false</span><span class="p">,</span><span class="cm" style="color: #998; font-style: italic;">/*genestrand*/</span><span class="mi" style="color: #099;">0</span><span class="p">,</span></span>
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4148
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<pre style="margin: 0;">+<span id="LC4148" class="line" lang="c"> <span class="n" style="color: #333;">want_lowest_coordinate_p</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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4149
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<pre style="margin: 0;">+<span id="LC4149" class="line" lang="c"> <span class="n" style="color: #333;">ninserts</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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4150
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<pre style="margin: 0;">+<span id="LC4150" class="line" lang="c"> <span class="n" style="color: #333;">nindels</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">adj</span><span class="p">;</span></span>
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4151
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<pre style="margin: 0;">+<span id="LC4151" class="line" lang="c"> <span class="n" style="color: #333;">total_nmatches</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">querylength</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">best_nmismatches_i</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">best_nmismatches_j</span><span class="p">;</span></span>
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4152
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<pre style="margin: 0;">+<span id="LC4152" class="line" lang="c"> <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;">adj</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>
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4153
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<pre style="margin: 0;">+<span id="LC4153" class="line" lang="c"> <span class="p">(</span><span class="n" style="color: #333;">indel_pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Indel_resolve_middle_insertion</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">best_nmismatches_i</span><span class="p">,</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">best_nmismatches_j</span><span class="p">,</span></span>
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4154
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<pre style="margin: 0;">+<span id="LC4154" class="line" lang="c"> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">best_ref_nmismatches_i</span><span class="p">,</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">best_ref_nmismatches_j</span><span class="p">,</span></span>
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4155
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<pre style="margin: 0;">+<span id="LC4155" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/*left*/</span><span class="n" style="color: #333;">tr_left0</span><span class="p">,</span><span class="cm" style="color: #998; font-style: italic;">/*indels*/</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">adj</span><span class="p">,</span></span>
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4156
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<pre style="margin: 0;">+<span id="LC4156" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/*mismatch_positions_left*/</span><span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span><span class="cm" style="color: #998; font-style: italic;">/*nmismatches_left*/</span><span class="mi" style="color: #099;">0</span><span class="p">,</span></span>
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4157
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<pre style="margin: 0;">+<span id="LC4157" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/*mismatch_positions_right*/</span><span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span><span class="cm" style="color: #998; font-style: italic;">/*nmismatches_right*/</span><span class="mi" style="color: #099;">0</span><span class="p">,</span></span>
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4158
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<pre style="margin: 0;">+<span id="LC4158" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/*ome*/</span><span class="n" style="color: #333;">transcriptomebits</span><span class="p">,</span><span class="cm" style="color: #998; font-style: italic;">/*ome_alt*/</span><span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span><span class="n" style="color: #333;">query_compress_rev</span><span class="p">,</span></span>
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4159
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<pre style="margin: 0;">+<span id="LC4159" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/*querystart*/</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="cm" style="color: #998; font-style: italic;">/*queryend*/</span><span class="n" style="color: #333;">querylength</span><span class="p">,</span><span class="n" style="color: #333;">querylength</span><span class="p">,</span></span>
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4160
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<pre style="margin: 0;">+<span id="LC4160" class="line" lang="c"> <span class="n" style="color: #333;">nmismatches_allowed</span><span class="p">,</span><span class="cm" style="color: #998; font-style: italic;">/*plusp*/</span><span class="nb" style="color: #0086b3;">false</span><span class="p">,</span><span class="cm" style="color: #998; font-style: italic;">/*genestrand*/</span><span class="mi" style="color: #099;">0</span><span class="p">,</span></span>
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4161
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<pre style="margin: 0;">+<span id="LC4161" class="line" lang="c"> <span class="n" style="color: #333;">want_lowest_coordinate_p</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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4162
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<pre style="margin: 0;">+<span id="LC4162" class="line" lang="c"> <span class="n" style="color: #333;">ninserts</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nindels</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">adj</span><span class="p">;</span></span>
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4163
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<pre style="margin: 0;">+<span id="LC4163" class="line" lang="c"> <span class="n" style="color: #333;">total_nmatches</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">querylength</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">best_nmismatches_i</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">best_nmismatches_j</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">ninserts</span><span class="p">;</span></span>
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4164
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<pre style="margin: 0;">+<span id="LC4164" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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4165
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<pre style="margin: 0;">+<span id="LC4165" class="line" lang="c"> <span class="n" style="color: #333;">adj</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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4166
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<pre style="margin: 0;">+<span id="LC4166" class="line" lang="c"> <span class="p">}</span></span>
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4154
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4167
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<pre style="margin: 0;"> <span id="LC4167" class="line" lang="c"> <span class="p">}</span></span>
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4168
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<pre style="margin: 0;">+<span id="LC4168" class="line" lang="c"> <span class="p">}</span></span>
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4155
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4169
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<pre style="margin: 0;"> <span id="LC4169" class="line" lang="c"> </span>
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4156
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<pre style="margin: 0;">-<span id="LC4156" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">adj</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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4157
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<pre style="margin: 0;">-<span id="LC4157" class="line" lang="c"> <span class="n" style="color: #333;">nexons</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Transcriptome_exons</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">exonbounds</span><span class="p">,</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">exonstarts</span><span class="p">,</span><span class="n" style="color: #333;">transcriptome</span><span class="p">,</span><span class="n" style="color: #333;">trnum</span><span class="p">);</span></span>
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4158
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<pre style="margin: 0;">-<span id="LC4158" class="line" lang="c"> <span class="n" style="color: #333;">Univ_IIT_interval_bounds</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">chroffset</span><span class="p">,</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">chrhigh</span><span class="p">,</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">chrlength</span><span class="p">,</span><span class="n" style="color: #333;">chromosome_iit</span><span class="p">,</span><span class="n" style="color: #333;">chrnum</span><span class="p">,</span><span class="n" style="color: #333;">circular_typeint</span><span class="p">);</span></span>
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4159
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<pre style="margin: 0;">-<span id="LC4159" class="line" lang="c"></span>
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4160
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<pre style="margin: 0;">-<span id="LC4160" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">transcript_genestrand</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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4161
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<pre style="margin: 0;">-<span id="LC4161" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Case 3 ultrafast gap: tminus, gplus. transcript_plusp == false && transcript_genestrand > 0 */</span></span>
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4162
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<pre style="margin: 0;">-<span id="LC4162" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"Case 3 ultrafast gap: tminus, gplus</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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4163
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<pre style="margin: 0;">-<span id="LC4163" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* sensedir = SENSE_ANTI; */</span></span>
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4164
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<pre style="margin: 0;">-<span id="LC4164" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* plusp = false; */</span></span>
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4165
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<pre style="margin: 0;">-<span id="LC4165" class="line" lang="c"></span>
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4166
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<pre style="margin: 0;">-<span id="LC4166" class="line" lang="c"> <span class="n" style="color: #333;">endpoints</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">Uintlist_T</span><span class="p">)</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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4167
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<pre style="margin: 0;">-<span id="LC4167" class="line" lang="c"> <span class="n" style="color: #333;">gaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">Intlist_T</span><span class="p">)</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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4170
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<pre style="margin: 0;">+<span id="LC4170" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">adj</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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4171
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<pre style="margin: 0;">+<span id="LC4171" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Skip finding an indel */</span></span>
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4168
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4172
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<pre style="margin: 0;"> <span id="LC4172" class="line" lang="c"></span>
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4169
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<pre style="margin: 0;">-<span id="LC4169" class="line" lang="c"> <span class="n" style="color: #333;">transcript_diag0</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tr_left0</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">troffset</span><span class="p">;</span></span>
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4170
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<pre style="margin: 0;">-<span id="LC4170" class="line" lang="c"> <span class="n" style="color: #333;">transcript_diag1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tr_left1</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">troffset</span><span class="p">;</span></span>
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4173
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<pre style="margin: 0;">+<span id="LC4173" class="line" lang="c"> <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;">transcript_genestrand</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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4174
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<pre style="margin: 0;">+<span id="LC4174" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Case 3 ultrafast gap: tminus, gplus. transcript_plusp == false && transcript_genestrand > 0 */</span></span>
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4175
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<pre style="margin: 0;">+<span id="LC4175" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"Case 3 ultrafast gap: tminus, gplus</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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4176
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<pre style="margin: 0;">+<span id="LC4176" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* sensedir = SENSE_ANTI; */</span></span>
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4177
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<pre style="margin: 0;">+<span id="LC4177" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* plusp = false; */</span></span>
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4171
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4178
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<pre style="margin: 0;"> <span id="LC4178" class="line" lang="c"></span>
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4172
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<pre style="margin: 0;">-<span id="LC4172" class="line" lang="c"> <span class="n" style="color: #333;">abortp</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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4179
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<pre style="margin: 0;">+<span id="LC4179" class="line" lang="c"> <span class="n" style="color: #333;">nexons</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Transcriptome_exons</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">exonbounds</span><span class="p">,</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">exonstarts</span><span class="p">,</span><span class="n" style="color: #333;">transcriptome</span><span class="p">,</span><span class="n" style="color: #333;">trnum</span><span class="p">);</span></span>
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4180
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<pre style="margin: 0;">+<span id="LC4180" class="line" lang="c"> <span class="n" style="color: #333;">Univ_IIT_interval_bounds</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">chroffset</span><span class="p">,</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">chrhigh</span><span class="p">,</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">chrlength</span><span class="p">,</span><span class="n" style="color: #333;">chromosome_iit</span><span class="p">,</span><span class="n" style="color: #333;">chrnum</span><span class="p">,</span><span class="n" style="color: #333;">circular_typeint</span><span class="p">);</span></span>
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4173
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4181
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<pre style="margin: 0;"> <span id="LC4181" class="line" lang="c"></span>
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4174
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<pre style="margin: 0;">-<span id="LC4174" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* first part */</span></span>
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4175
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<pre style="margin: 0;">-<span id="LC4175" class="line" lang="c"> <span class="n" style="color: #333;">tr_left</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tr_left0</span><span class="p">;</span></span>
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4176
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<pre style="margin: 0;">-<span id="LC4176" class="line" lang="c"> <span class="n" style="color: #333;">queryend</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">querylength</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/* tminus: compute from queryend to querystart */</span></span>
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4177
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<pre style="margin: 0;">-<span id="LC4177" class="line" lang="c"> <span class="n" style="color: #333;">querystart</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">querylength</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">indel_pos</span><span class="p">;</span></span>
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4178
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<pre style="margin: 0;">-<span id="LC4178" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</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;">Analyzing query %d..%d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">querystart</span><span class="p">,</span><span class="n" style="color: #333;">queryend</span><span class="p">));</span></span>
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4179
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<pre style="margin: 0;">-<span id="LC4179" class="line" lang="c"> </span>
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4180
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<pre style="margin: 0;">-<span id="LC4180" class="line" lang="c"> <span class="n" style="color: #333;">overall_trstart</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">trstart</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">transcript_diag0</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="n" style="color: #333;">querylength</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">queryend</span><span class="p">);</span> <span class="cm" style="color: #998; font-style: italic;">/* tminus */</span></span>
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4182
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<pre style="margin: 0;">+<span id="LC4182" class="line" lang="c"> <span class="n" style="color: #333;">endpoints</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">Uintlist_T</span><span class="p">)</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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4183
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<pre style="margin: 0;">+<span id="LC4183" class="line" lang="c"> <span class="n" style="color: #333;">gaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">Intlist_T</span><span class="p">)</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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4184
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<pre style="margin: 0;">+<span id="LC4184" class="line" lang="c"> <span class="n" style="color: #333;">abortp</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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4185
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<pre style="margin: 0;">+<span id="LC4185" class="line" lang="c"> </span>
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4186
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<pre style="margin: 0;">+<span id="LC4186" class="line" lang="c"> <span class="n" style="color: #333;">transcript_diag0</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tr_left0</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">troffset</span><span class="p">;</span></span>
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4187
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<pre style="margin: 0;">+<span id="LC4187" class="line" lang="c"> <span class="n" style="color: #333;">transcript_diag1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tr_left1</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">troffset</span><span class="p">;</span></span>
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4188
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<pre style="margin: 0;">+<span id="LC4188" class="line" lang="c"> </span>
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4189
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<pre style="margin: 0;">+<span id="LC4189" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* first part */</span></span>
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4190
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<pre style="margin: 0;">+<span id="LC4190" class="line" lang="c"> <span class="n" style="color: #333;">tr_left</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tr_left0</span><span class="p">;</span></span>
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4191
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<pre style="margin: 0;">+<span id="LC4191" class="line" lang="c"> <span class="n" style="color: #333;">queryend</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">querylength</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/* tminus: compute from queryend to querystart */</span></span>
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4192
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<pre style="margin: 0;">+<span id="LC4192" class="line" lang="c"> <span class="n" style="color: #333;">querystart</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">querylength</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">indel_pos</span><span class="p">;</span></span>
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4193
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<pre style="margin: 0;">+<span id="LC4193" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</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;">Analyzing query %d..%d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">querystart</span><span class="p">,</span><span class="n" style="color: #333;">queryend</span><span class="p">));</span></span>
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4194
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<pre style="margin: 0;">+<span id="LC4194" class="line" lang="c"> </span>
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4195
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<pre style="margin: 0;">+<span id="LC4195" class="line" lang="c"> <span class="n" style="color: #333;">overall_trstart</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">trstart</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">transcript_diag0</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="n" style="color: #333;">querylength</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">queryend</span><span class="p">);</span> <span class="cm" style="color: #998; font-style: italic;">/* tminus */</span></span>
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4181
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4196
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<pre style="margin: 0;"> <span id="LC4196" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifdef DEBUG2</span></span>
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4182
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<td class="diff-line-num new_line old" data-linenumber="4197" 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="LC4182" class="line" lang="c"> <span class="idiff left right"> </span><span class="n" style="color: #333;">trend</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">transcript_diag0</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="n" style="color: #333;">querylength</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">querystart</span><span class="p">);</span> <span class="cm" style="color: #998; font-style: italic;">/* tminus */</span></span>
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4183
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<td class="diff-line-num new_line old" data-linenumber="4197" 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="LC4183" class="line" lang="c"> <span class="idiff left right"> </span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"transcript_diag %d, trstart %d, trend %d, tr_left %u, adj %d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span></span>
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4184
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<pre style="margin: 0;">-<span id="LC4184" class="line" lang="c"> <span class="idiff left right"> </span><span class="n" style="color: #333;">transcript_diag0</span><span class="p">,</span><span class="n" style="color: #333;">trstart</span><span class="p">,</span><span class="n" style="color: #333;">trend</span><span class="p">,</span><span class="n" style="color: #333;">tr_left</span><span class="p">,</span><span class="n" style="color: #333;">adj</span><span class="p">);</span></span>
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4197
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<pre style="margin: 0;">+<span id="LC4197" class="line" lang="c"> <span class="n" style="color: #333;">trend</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">transcript_diag0</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="n" style="color: #333;">querylength</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">querystart</span><span class="p">);</span> <span class="cm" style="color: #998; font-style: italic;">/* tminus */</span></span>
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4198
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<pre style="margin: 0;">+<span id="LC4198" class="line" lang="c"> <span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"transcript_diag %d, trstart %d, trend %d, tr_left %u, adj %d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span></span>
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4199
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<pre style="margin: 0;">+<span id="LC4199" class="line" lang="c"> <span class="n" style="color: #333;">transcript_diag0</span><span class="p">,</span><span class="n" style="color: #333;">trstart</span><span class="p">,</span><span class="n" style="color: #333;">trend</span><span class="p">,</span><span class="n" style="color: #333;">tr_left</span><span class="p">,</span><span class="n" style="color: #333;">adj</span><span class="p">);</span></span>
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4185
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4200
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<pre style="margin: 0;"> <span id="LC4200" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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4186
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4201
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<pre style="margin: 0;"> <span id="LC4201" class="line" lang="c"> </span>
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4187
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<pre style="margin: 0;">-<span id="LC4187" class="line" lang="c"> <span class="idiff left right"> </span><span class="n" style="color: #333;">exoni</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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4202
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<pre style="margin: 0;">+<span id="LC4202" class="line" lang="c"> <span class="n" style="color: #333;">exoni</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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4188
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4203
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<pre style="margin: 0;"> <span id="LC4203" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;">#if 0 && defined(HAVE_AVX2)</span></span>
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4189
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<pre style="margin: 0;">-<span id="LC4189" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> <span class="idiff left right"> </span>_trstart = _mm256_set1_epi32(trstart);</span></span>
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4190
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<pre style="margin: 0;">-<span id="LC4190" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> <span class="idiff left right"> </span>ptr = exonbounds;</span></span>
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4191
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<pre style="margin: 0;">-<span id="LC4191" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> <span class="idiff left right"> </span>_exonbounds = _mm256_loadu_si256((__m256i *) ptr);</span></span>
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4192
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<pre style="margin: 0;">-<span id="LC4192" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> <span class="idiff left right"> </span>_diff = _mm256_cmpgt_epi32(_exonbounds,_trstart);</span></span>
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4193
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<pre style="margin: 0;">-<span id="LC4193" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> <span class="idiff left right"> </span>while (all_zero_p(_diff)) {</span></span>
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4194
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<pre style="margin: 0;">-<span id="LC4194" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> <span class="idiff left right"> </span>exoni += 8;</span></span>
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4195
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<pre style="margin: 0;">-<span id="LC4195" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> <span class="idiff left right"> </span>ptr += 8;</span></span>
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4196
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<pre style="margin: 0;">-<span id="LC4196" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> <span class="idiff left right"> </span>_exonbounds = _mm256_loadu_si256((__m256i *) ptr);</span></span>
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4197
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<td class="diff-line-num new_line old" data-linenumber="4204" 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="LC4197" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> <span class="idiff left right"> </span>_diff = _mm256_cmpgt_epi32(_exonbounds,_trstart);</span></span>
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4198
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<pre style="margin: 0;">-<span id="LC4198" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> <span class="idiff left right"> </span>}</span></span>
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4199
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<pre style="margin: 0;">-<span id="LC4199" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> <span class="idiff left right"> </span>matchbits = _mm256_movemask_ps(_mm256_castsi256_ps(_diff));</span></span>
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4200
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<pre style="margin: 0;">-<span id="LC4200" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> <span class="idiff left right"> </span>exoni += count_trailing_zeroes_32(matchbits);</span></span>
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4204
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<pre style="margin: 0;">+<span id="LC4204" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> _trstart = _mm256_set1_epi32(trstart);</span></span>
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4205
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<pre style="margin: 0;">+<span id="LC4205" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> ptr = exonbounds;</span></span>
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4206
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<pre style="margin: 0;">+<span id="LC4206" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> _exonbounds = _mm256_loadu_si256((__m256i *) ptr);</span></span>
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4207
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<pre style="margin: 0;">+<span id="LC4207" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> _diff = _mm256_cmpgt_epi32(_exonbounds,_trstart);</span></span>
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4208
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<pre style="margin: 0;">+<span id="LC4208" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> while (all_zero_p(_diff)) {</span></span>
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4209
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<pre style="margin: 0;">+<span id="LC4209" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> <span class="idiff left right"> </span>exoni += 8;</span></span>
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4210
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<pre style="margin: 0;">+<span id="LC4210" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> <span class="idiff left right"> </span>ptr += 8;</span></span>
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4211
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<pre style="margin: 0;">+<span id="LC4211" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> <span class="idiff left right"> </span>_exonbounds = _mm256_loadu_si256((__m256i *) ptr);</span></span>
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4212
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<pre style="margin: 0;">+<span id="LC4212" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> <span class="idiff left right"> </span>_diff = _mm256_cmpgt_epi32(_exonbounds,_trstart);</span></span>
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4213
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<pre style="margin: 0;">+<span id="LC4213" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> }</span></span>
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4214
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<pre style="margin: 0;">+<span id="LC4214" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> matchbits = _mm256_movemask_ps(_mm256_castsi256_ps(_diff));</span></span>
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4215
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<pre style="margin: 0;">+<span id="LC4215" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> exoni += count_trailing_zeroes_32(matchbits);</span></span>
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4201
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4216
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<pre style="margin: 0;"> <span id="LC4216" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;">#elif</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">defined</span><span class="p">(</span><span class="n" style="color: #333;">HAVE_SSE2</span><span class="p">)</span></span>
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4202
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<pre style="margin: 0;">-<span id="LC4202" class="line" lang="c"> <span class="idiff left right"> </span><span class="n" style="color: #333;">_trstart</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_set1_epi32</span><span class="p">(</span><span class="n" style="color: #333;">trstart</span><span class="p">);</span></span>
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4203
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<pre style="margin: 0;">-<span id="LC4203" class="line" lang="c"> <span class="idiff left right"> </span><span class="n" style="color: #333;">ptr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">exonbounds</span><span class="p">;</span></span>
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4204
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<pre style="margin: 0;">-<span id="LC4204" class="line" lang="c"> <span class="idiff left right"> </span><span class="n" style="color: #333;">_exonbounds</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_loadu_si128</span><span class="p">((</span><span class="n" style="color: #333;">__m128i</span> <span class="o" style="font-weight: 600;">*</span><span class="p">)</span> <span class="n" style="color: #333;">ptr</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4205" 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">
4205
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<td class="diff-line-num new_line old" data-linenumber="4217" 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="LC4205" class="line" lang="c"> <span class="idiff left right"> </span><span class="n" style="color: #333;">_diff</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_cmpgt_epi32</span><span class="p">(</span><span class="n" style="color: #333;">_exonbounds</span><span class="p">,</span><span class="n" style="color: #333;">_trstart</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4206" 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">
4206
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<td class="diff-line-num new_line old" data-linenumber="4217" 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="LC4206" class="line" lang="c"> <span class="idiff left right"> </span><span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">all_zero_p</span><span class="p">(</span><span class="n" style="color: #333;">_diff</span><span class="p">))</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4207" 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">
4207
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<td class="diff-line-num new_line old" data-linenumber="4217" 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="LC4207" class="line" lang="c"> <span class="idiff left right"> </span><span class="n" style="color: #333;">exoni</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">4</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4208" 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">
4208
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<td class="diff-line-num new_line old" data-linenumber="4217" 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="LC4208" class="line" lang="c"> <span class="idiff left right"> </span><span class="n" style="color: #333;">ptr</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">4</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4209" 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">
4209
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<td class="diff-line-num new_line old" data-linenumber="4217" 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="LC4209" class="line" lang="c"> <span class="idiff left right"> </span><span class="n" style="color: #333;">_exonbounds</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_loadu_si128</span><span class="p">((</span><span class="n" style="color: #333;">__m128i</span> <span class="o" style="font-weight: 600;">*</span><span class="p">)</span> <span class="n" style="color: #333;">ptr</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4210" 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">
4210
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<td class="diff-line-num new_line old" data-linenumber="4217" 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="LC4210" class="line" lang="c"> <span class="idiff left right"> </span><span class="n" style="color: #333;">_diff</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_cmpgt_epi32</span><span class="p">(</span><span class="n" style="color: #333;">_exonbounds</span><span class="p">,</span><span class="n" style="color: #333;">_trstart</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4211" 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">
4211
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<td class="diff-line-num new_line old" data-linenumber="4217" 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="LC4211" class="line" lang="c"> <span class="idiff left right"> </span><span class="p">}</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4212" 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">
4212
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<td class="diff-line-num new_line old" data-linenumber="4217" 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="LC4212" class="line" lang="c"> <span class="idiff left right"> </span><span class="n" style="color: #333;">matchbits</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_movemask_ps</span><span class="p">(</span><span class="n" style="color: #333;">_mm_castsi128_ps</span><span class="p">(</span><span class="n" style="color: #333;">_diff</span><span class="p">));</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4213" 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">
4213
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<td class="diff-line-num new_line old" data-linenumber="4217" 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="LC4213" class="line" lang="c"> <span class="idiff left right"> </span><span class="n" style="color: #333;">exoni</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">count_trailing_zeroes_32</span><span class="p">(</span><span class="n" style="color: #333;">matchbits</span><span class="p">);</span></span>
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<td class="diff-line-num new old_line" data-linenumber="4214" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="4217" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4217
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<pre style="margin: 0;">+<span id="LC4217" class="line" lang="c"> <span class="n" style="color: #333;">_trstart</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_set1_epi32</span><span class="p">(</span><span class="n" style="color: #333;">trstart</span><span class="p">);</span></span>
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<td class="diff-line-num new old_line" data-linenumber="4214" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="4218" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4218
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<pre style="margin: 0;">+<span id="LC4218" class="line" lang="c"> <span class="n" style="color: #333;">ptr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">exonbounds</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4219" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4219
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<pre style="margin: 0;">+<span id="LC4219" class="line" lang="c"> <span class="n" style="color: #333;">_exonbounds</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_loadu_si128</span><span class="p">((</span><span class="n" style="color: #333;">__m128i</span> <span class="o" style="font-weight: 600;">*</span><span class="p">)</span> <span class="n" style="color: #333;">ptr</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4220" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4220
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<pre style="margin: 0;">+<span id="LC4220" class="line" lang="c"> <span class="n" style="color: #333;">_diff</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_cmpgt_epi32</span><span class="p">(</span><span class="n" style="color: #333;">_exonbounds</span><span class="p">,</span><span class="n" style="color: #333;">_trstart</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4221" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4221
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<pre style="margin: 0;">+<span id="LC4221" class="line" lang="c"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">all_zero_p</span><span class="p">(</span><span class="n" style="color: #333;">_diff</span><span class="p">))</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4222" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4222
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<pre style="margin: 0;">+<span id="LC4222" class="line" lang="c"> <span class="idiff left right"> </span><span class="n" style="color: #333;">exoni</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">4</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4223" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4223
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<pre style="margin: 0;">+<span id="LC4223" class="line" lang="c"> <span class="idiff left right"> </span><span class="n" style="color: #333;">ptr</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">4</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4224" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4224
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<pre style="margin: 0;">+<span id="LC4224" class="line" lang="c"> <span class="idiff left right"> </span><span class="n" style="color: #333;">_exonbounds</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_loadu_si128</span><span class="p">((</span><span class="n" style="color: #333;">__m128i</span> <span class="o" style="font-weight: 600;">*</span><span class="p">)</span> <span class="n" style="color: #333;">ptr</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4225" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4225
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<pre style="margin: 0;">+<span id="LC4225" class="line" lang="c"> <span class="idiff left right"> </span><span class="n" style="color: #333;">_diff</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_cmpgt_epi32</span><span class="p">(</span><span class="n" style="color: #333;">_exonbounds</span><span class="p">,</span><span class="n" style="color: #333;">_trstart</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4226" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4226
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<pre style="margin: 0;">+<span id="LC4226" class="line" lang="c"> <span class="p">}</span></span>
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4227
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<pre style="margin: 0;">+<span id="LC4227" class="line" lang="c"> <span class="n" style="color: #333;">matchbits</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_movemask_ps</span><span class="p">(</span><span class="n" style="color: #333;">_mm_castsi128_ps</span><span class="p">(</span><span class="n" style="color: #333;">_diff</span><span class="p">));</span></span>
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4228
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<pre style="margin: 0;">+<span id="LC4228" class="line" lang="c"> <span class="n" style="color: #333;">exoni</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">count_trailing_zeroes_32</span><span class="p">(</span><span class="n" style="color: #333;">matchbits</span><span class="p">);</span></span>
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4214
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<td class="diff-line-num new_line" data-linenumber="4229" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4229
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<pre style="margin: 0;"> <span id="LC4229" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#else</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4215" 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">
4215
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<td class="diff-line-num new_line old" data-linenumber="4230" 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="LC4215" class="line" lang="c"> <span class="idiff left right"> </span><span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">exoni</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">nexons</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">exonbounds</span><span class="p">[</span><span class="n" style="color: #333;">exoni</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">trstart</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4216" 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">
4216
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<td class="diff-line-num new_line old" data-linenumber="4230" 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="LC4216" class="line" lang="c"> <span class="idiff left right"> </span><span class="n" style="color: #333;">exoni</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4217" 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">
4217
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<td class="diff-line-num new_line old" data-linenumber="4230" 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="LC4217" class="line" lang="c"> <span class="idiff left right"> </span><span class="p">}</span></span>
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<td class="diff-line-num new old_line" data-linenumber="4218" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="4230" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4230
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<pre style="margin: 0;">+<span id="LC4230" class="line" lang="c"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">exoni</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">nexons</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">exonbounds</span><span class="p">[</span><span class="n" style="color: #333;">exoni</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">trstart</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4231" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4231
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<pre style="margin: 0;">+<span id="LC4231" class="line" lang="c"> <span class="idiff left right"> </span><span class="n" style="color: #333;">exoni</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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4232
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<pre style="margin: 0;">+<span id="LC4232" class="line" lang="c"> <span class="p">}</span></span>
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4218
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<td class="diff-line-num new_line" data-linenumber="4233" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4233
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<pre style="margin: 0;"> <span id="LC4233" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4219" 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">
4219
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<td class="diff-line-num new_line old" data-linenumber="4234" 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="LC4219" class="line" lang="c"></span>
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<td class="diff-line-num old old_line" data-linenumber="4220" 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">
4220
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<td class="diff-line-num new_line old" data-linenumber="4234" 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="LC4220" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">exoni</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">nexons</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4221" 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">
4221
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<td class="diff-line-num new_line old" data-linenumber="4234" 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="LC4221" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"ABORTING BECAUSE OF EXONI %d >= NEXONS %d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">exoni</span><span class="p">,</span><span class="n" style="color: #333;">nexons</span><span class="p">));</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4222" 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">
4222
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<td class="diff-line-num new_line old" data-linenumber="4234" 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="LC4222" class="line" lang="c"> <span class="n" style="color: #333;">abortp</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4223" 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">
4223
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<td class="diff-line-num new_line old" data-linenumber="4234" 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="LC4223" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4224" 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">
4224
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<td class="diff-line-num new_line old" data-linenumber="4234" 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="LC4224" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"(13) exoni %d out of nexons %d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">exoni</span><span class="p">,</span><span class="n" style="color: #333;">nexons</span><span class="p">));</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4225" 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">
4225
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<td class="diff-line-num new_line old" data-linenumber="4234" 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="LC4225" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">exoni</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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4226
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<td class="diff-line-num new_line old" data-linenumber="4234" 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="LC4226" class="line" lang="c"> <span class="n" style="color: #333;">exonpos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">trstart</span><span class="p">;</span></span>
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4227
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<td class="diff-line-num new_line old" data-linenumber="4234" 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="LC4227" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4228" 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">
4228
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<td class="diff-line-num new_line old" data-linenumber="4234" 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="LC4228" class="line" lang="c"> <span class="n" style="color: #333;">exonpos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">trstart</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">exonbounds</span><span class="p">[</span><span class="n" style="color: #333;">exoni</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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4229
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<pre style="margin: 0;">-<span id="LC4229" class="line" lang="c"> <span class="p">}</span></span>
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4230
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<pre style="margin: 0;">-<span id="LC4230" class="line" lang="c"> <span class="n" style="color: #333;">exon_residual</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">exonbounds</span><span class="p">[</span><span class="n" style="color: #333;">exoni</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">trstart</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4231" 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">
4231
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<td class="diff-line-num new_line old" data-linenumber="4234" 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="LC4231" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"exoni %d => exon_residual %d, exonpos %d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">exoni</span><span class="p">,</span><span class="n" style="color: #333;">exon_residual</span><span class="p">,</span><span class="n" style="color: #333;">exonpos</span><span class="p">));</span></span>
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4232
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<td class="diff-line-num new_line old" data-linenumber="4234" 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="LC4232" class="line" lang="c"></span>
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<td class="diff-line-num old old_line" data-linenumber="4233" 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">
4233
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<td class="diff-line-num new_line old" data-linenumber="4234" 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="LC4233" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Generate one substring per exon */</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4234" 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">
4234
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<td class="diff-line-num new_line old" data-linenumber="4234" 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="LC4234" class="line" lang="c"> <span class="n" style="color: #333;">genomicpos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">exonstarts</span><span class="p">[</span><span class="n" style="color: #333;">exoni</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">exonpos</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/* gplus */</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4235" 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">
4235
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<td class="diff-line-num new_line old" data-linenumber="4234" 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="LC4235" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"genomicpos %u = %u + %u - 1</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">genomicpos</span><span class="p">,</span><span class="n" style="color: #333;">exonstarts</span><span class="p">[</span><span class="n" style="color: #333;">exoni</span><span class="p">],</span><span class="n" style="color: #333;">exonpos</span><span class="p">));</span></span>
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4236
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<td class="diff-line-num new_line old" data-linenumber="4234" 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="LC4236" class="line" lang="c"> <span class="n" style="color: #333;">align_residual</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">queryend</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">querystart</span><span class="p">;</span></span>
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4237
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<td class="diff-line-num new_line old" data-linenumber="4234" 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="LC4237" class="line" lang="c"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">align_residual</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4238" 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">
4238
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<td class="diff-line-num new_line old" data-linenumber="4234" 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="LC4238" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"abortp %d,align_residual %d, exon_residual %d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">abortp</span><span class="p">,</span><span class="n" style="color: #333;">align_residual</span><span class="p">,</span><span class="n" style="color: #333;">exon_residual</span><span class="p">));</span></span>
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4239
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<td class="diff-line-num new_line old" data-linenumber="4234" 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="LC4239" class="line" lang="c"> <span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">align_residual</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">exon_residual</span><span class="p">)</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">align_residual</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">exon_residual</span><span class="p">;</span></span>
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4240
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<td class="diff-line-num new_line old" data-linenumber="4234" 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="LC4240" class="line" lang="c"> <span class="n" style="color: #333;">querystart</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">queryend</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">len</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/* tminus */</span></span>
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4241
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<td class="diff-line-num new_line old" data-linenumber="4234" 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="LC4241" class="line" lang="c"> </span>
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4242
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<td class="diff-line-num new_line old" data-linenumber="4234" 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="LC4242" class="line" lang="c"> <span class="n" style="color: #333;">alignend</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">chroffset</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">genomicpos</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4243" 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">
4243
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<td class="diff-line-num new_line old" data-linenumber="4234" 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="LC4243" class="line" lang="c"> <span class="n" style="color: #333;">alignstart</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alignend</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">len</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/* gplus */</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4244" 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">
4244
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<td class="diff-line-num new_line old" data-linenumber="4234" 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="LC4244" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">left</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alignend</span> <span class="o" style="font-weight: 600;">-</span> <span class="p">(</span><span class="n" style="color: #333;">querylength</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">queryend</span><span class="p">));</span> <span class="cm" style="color: #998; font-style: italic;">/* tminus != gplus */</span></span>
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4245
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<td class="diff-line-num new_line old" data-linenumber="4234" 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="LC4245" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"tr ultrafast gap case 3 1st part query %d..%d, align %u..%u [%u..%u], left %u = %u - (%d - %d)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4246" 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">
4246
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<td class="diff-line-num new_line old" data-linenumber="4234" 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="LC4246" class="line" lang="c"> <span class="n" style="color: #333;">querystart</span><span class="p">,</span><span class="n" style="color: #333;">queryend</span><span class="p">,</span><span class="n" style="color: #333;">alignstart</span><span class="p">,</span><span class="n" style="color: #333;">alignend</span><span class="p">,</span><span class="n" style="color: #333;">alignstart</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">chroffset</span><span class="p">,</span><span class="n" style="color: #333;">alignend</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">chroffset</span><span class="p">,</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4247" 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">
4247
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<td class="diff-line-num new_line old" data-linenumber="4234" 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="LC4247" class="line" lang="c"> <span class="n" style="color: #333;">left</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">chroffset</span><span class="p">,</span><span class="n" style="color: #333;">alignend</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">chroffset</span><span class="p">,</span><span class="n" style="color: #333;">querylength</span><span class="p">,</span><span class="n" style="color: #333;">queryend</span><span class="p">));</span></span>
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4248
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<pre style="margin: 0;">-<span id="LC4248" class="line" lang="c"></span>
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<td class="diff-line-num old old_line" data-linenumber="4249" 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">
4249
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<td class="diff-line-num new_line old" data-linenumber="4234" 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="LC4249" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* tminus: plus alignend first */</span></span>
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4250
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<td class="diff-line-num new_line old" data-linenumber="4234" 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="LC4250" class="line" lang="c"> <span class="n" style="color: #333;">endpoints</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Uintlist_push</span><span class="p">(</span><span class="n" style="color: #333;">endpoints</span><span class="p">,(</span><span class="n" style="color: #333;">Chrpos_T</span><span class="p">)</span> <span class="p">(</span><span class="n" style="color: #333;">alignend</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">chroffset</span><span class="p">));</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4251" 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">
4251
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<td class="diff-line-num new_line old" data-linenumber="4234" 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="LC4251" class="line" lang="c"> <span class="n" style="color: #333;">endpoints</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Uintlist_push</span><span class="p">(</span><span class="n" style="color: #333;">endpoints</span><span class="p">,(</span><span class="n" style="color: #333;">Chrpos_T</span><span class="p">)</span> <span class="p">(</span><span class="n" style="color: #333;">alignstart</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">chroffset</span><span class="p">));</span></span>
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4252
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<pre style="margin: 0;">-<span id="LC4252" class="line" lang="c"></span>
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<td class="diff-line-num old old_line" data-linenumber="4253" 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">
4253
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<td class="diff-line-num new_line old" data-linenumber="4234" 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="LC4253" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">align_residual</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">exon_residual</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4254" 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">
4254
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<td class="diff-line-num new_line old" data-linenumber="4234" 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="LC4254" class="line" lang="c"> <span class="n" style="color: #333;">exon_residual</span> <span class="o" style="font-weight: 600;">-=</span> <span class="n" style="color: #333;">align_residual</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/* Need to know this if we have a following deletion */</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4255" 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">
4255
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<td class="diff-line-num new_line old" data-linenumber="4234" 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="LC4255" class="line" lang="c"> <span class="n" style="color: #333;">align_residual</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4256" 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">
4256
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<td class="diff-line-num new_line old" data-linenumber="4234" 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="LC4256" class="line" lang="c"> <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="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">exoni</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">nexons</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4257" 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">
4257
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<td class="diff-line-num new_line old" data-linenumber="4234" 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="LC4257" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Aligning past the end of the transcript */</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4258" 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">
4258
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<td class="diff-line-num new_line old" data-linenumber="4234" 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="LC4258" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"6 ABORTING BECAUSE ALIGNING PAST END OF TRANSCRIPT</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">));</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4259" 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">
4259
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<td class="diff-line-num new_line old" data-linenumber="4234" 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="LC4259" class="line" lang="c"> <span class="n" style="color: #333;">align_residual</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4260" 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">
4260
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<td class="diff-line-num new_line old" data-linenumber="4234" 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="LC4260" class="line" lang="c"> <span class="n" style="color: #333;">abortp</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4261" 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">
4261
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<td class="diff-line-num new_line old" data-linenumber="4234" 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="LC4261" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4262" 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">
4262
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<td class="diff-line-num new_line old" data-linenumber="4234" 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="LC4262" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* nintrons += 1; */</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4263" 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">
4263
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<td class="diff-line-num new_line old" data-linenumber="4234" 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="LC4263" class="line" lang="c"> <span class="n" style="color: #333;">align_residual</span> <span class="o" style="font-weight: 600;">-=</span> <span class="n" style="color: #333;">len</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4264" 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">
4264
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<td class="diff-line-num new_line old" data-linenumber="4234" 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="LC4264" class="line" lang="c"> <span class="n" style="color: #333;">queryend</span> <span class="o" style="font-weight: 600;">-=</span> <span class="n" style="color: #333;">len</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/* tminus */</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4265" 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">
4265
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<td class="diff-line-num new_line old" data-linenumber="4234" 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="LC4265" class="line" lang="c"> <span class="n" style="color: #333;">genomicpos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">exonstarts</span><span class="p">[</span><span class="n" style="color: #333;">exoni</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="cm" style="color: #998; font-style: italic;">/* gplus */</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4266" 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">
4266
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<td class="diff-line-num new_line old" data-linenumber="4234" 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="LC4266" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"genomicpos %u = %u - 1</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">genomicpos</span><span class="p">,</span><span class="n" style="color: #333;">exonstarts</span><span class="p">[</span><span class="n" style="color: #333;">exoni</span><span class="p">]));</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4267" 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">
4267
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<td class="diff-line-num new_line old" data-linenumber="4234" 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="LC4267" class="line" lang="c"> <span class="n" style="color: #333;">exon_residual</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">exonbounds</span><span class="p">[</span><span class="n" style="color: #333;">exoni</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">exonbounds</span><span class="p">[</span><span class="n" style="color: #333;">exoni</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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4268
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<pre style="margin: 0;">-<span id="LC4268" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"INTRON</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">));</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4269" 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">
4269
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<td class="diff-line-num new_line old" data-linenumber="4234" 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="LC4269" class="line" lang="c"> <span class="n" style="color: #333;">gaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Intlist_push</span><span class="p">(</span><span class="n" style="color: #333;">gaps</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4270" 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">
4270
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<td class="diff-line-num new_line old" data-linenumber="4234" 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="LC4270" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4271" 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">
4271
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<td class="diff-line-num new_line old" data-linenumber="4234" 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="LC4271" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4272" 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">
4272
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<td class="diff-line-num new_line old" data-linenumber="4234" 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="LC4272" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4273" 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">
4273
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<td class="diff-line-num new_line old" data-linenumber="4234" 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="LC4273" class="line" lang="c"></span>
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<td class="diff-line-num old old_line" data-linenumber="4274" 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">
4274
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<td class="diff-line-num new_line old" data-linenumber="4234" 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="LC4274" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* gap */</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4275" 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">
4275
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<td class="diff-line-num new_line old" data-linenumber="4234" 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="LC4275" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"INDEL: last piece %d | nindels %d | next piece %d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">len</span><span class="p">,</span><span class="n" style="color: #333;">nindels</span><span class="p">,</span><span class="n" style="color: #333;">exon_residual</span><span class="p">));</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="4276" 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">
4276
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<td class="diff-line-num new_line old" data-linenumber="4234" 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="LC4276" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"exon residual %d vs nindels %d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">exon_residual</span><span class="p">,</span><span class="n" style="color: #333;">nindels</span><span class="p">));</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="4277" 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">
4277
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<td class="diff-line-num new_line old" data-linenumber="4234" 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="LC4277" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">abortp</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4278" 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">
4278
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<td class="diff-line-num new_line old" data-linenumber="4234" 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="LC4278" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Skip */</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4279" 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">
4279
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<td class="diff-line-num new_line old" data-linenumber="4234" 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="LC4279" class="line" lang="c"> <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="cm" style="color: #998; font-style: italic;">/*len <= nindels ||*/</span><span class="n" style="color: #333;">exon_residual</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">nindels</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4280" 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">
4280
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<td class="diff-line-num new_line old" data-linenumber="4234" 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="LC4280" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"ABORTING BECAUSE INDEL OVERLAPS SPLICE SITE</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">));</span></span>
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<td class="diff-line-num new old_line" data-linenumber="4281" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="4234" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4234
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<pre style="margin: 0;">+<span id="LC4234" class="line" lang="c"> </span>
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<td class="diff-line-num new new_line" data-linenumber="4235" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4235
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<pre style="margin: 0;">+<span id="LC4235" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">exoni</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">nexons</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new old_line" data-linenumber="4281" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="4236" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4236
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<pre style="margin: 0;">+<span id="LC4236" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"ABORTING BECAUSE OF EXONI %d >= NEXONS %d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">exoni</span><span class="p">,</span><span class="n" style="color: #333;">nexons</span><span class="p">));</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4237" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4237
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<pre style="margin: 0;">+<span id="LC4237" class="line" lang="c"> <span class="n" style="color: #333;">abortp</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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<td class="diff-line-num new old_line" data-linenumber="4281" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="4238" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4238
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<pre style="margin: 0;">+<span id="LC4238" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="4281" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="4239" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4239
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<pre style="margin: 0;">+<span id="LC4239" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"(13) exoni %d out of nexons %d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">exoni</span><span class="p">,</span><span class="n" style="color: #333;">nexons</span><span class="p">));</span></span>
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<td class="diff-line-num new old_line" data-linenumber="4281" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="4240" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4240
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<pre style="margin: 0;">+<span id="LC4240" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">exoni</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new old_line" data-linenumber="4281" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="4241" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4241
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<pre style="margin: 0;">+<span id="LC4241" class="line" lang="c"> <span class="n" style="color: #333;">exonpos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">trstart</span><span class="p">;</span></span>
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4242
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<pre style="margin: 0;">+<span id="LC4242" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4243" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4243
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<pre style="margin: 0;">+<span id="LC4243" class="line" lang="c"> <span class="n" style="color: #333;">exonpos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">trstart</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">exonbounds</span><span class="p">[</span><span class="n" style="color: #333;">exoni</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">];</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4244" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4244
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<pre style="margin: 0;">+<span id="LC4244" class="line" lang="c"> <span class="p">}</span></span>
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4245
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<pre style="margin: 0;">+<span id="LC4245" class="line" lang="c"> <span class="n" style="color: #333;">exon_residual</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">exonbounds</span><span class="p">[</span><span class="n" style="color: #333;">exoni</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">trstart</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4246" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4246
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<pre style="margin: 0;">+<span id="LC4246" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"exoni %d => exon_residual %d, exonpos %d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">exoni</span><span class="p">,</span><span class="n" style="color: #333;">exon_residual</span><span class="p">,</span><span class="n" style="color: #333;">exonpos</span><span class="p">));</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4247" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4247
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<pre style="margin: 0;">+<span id="LC4247" class="line" lang="c"> </span>
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<td class="diff-line-num new new_line" data-linenumber="4248" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4248
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<pre style="margin: 0;">+<span id="LC4248" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Generate one substring per exon */</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4249" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4249
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<pre style="margin: 0;">+<span id="LC4249" class="line" lang="c"> <span class="n" style="color: #333;">genomicpos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">exonstarts</span><span class="p">[</span><span class="n" style="color: #333;">exoni</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">exonpos</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/* gplus */</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4250" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4250
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<pre style="margin: 0;">+<span id="LC4250" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"genomicpos %u = %u + %u - 1</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">genomicpos</span><span class="p">,</span><span class="n" style="color: #333;">exonstarts</span><span class="p">[</span><span class="n" style="color: #333;">exoni</span><span class="p">],</span><span class="n" style="color: #333;">exonpos</span><span class="p">));</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4251" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4251
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<pre style="margin: 0;">+<span id="LC4251" class="line" lang="c"> <span class="n" style="color: #333;">align_residual</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">queryend</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">querystart</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4252" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4252
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<pre style="margin: 0;">+<span id="LC4252" class="line" lang="c"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">align_residual</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4253" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4253
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<pre style="margin: 0;">+<span id="LC4253" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"abortp %d,align_residual %d, exon_residual %d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">abortp</span><span class="p">,</span><span class="n" style="color: #333;">align_residual</span><span class="p">,</span><span class="n" style="color: #333;">exon_residual</span><span class="p">));</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4254" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4254
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<pre style="margin: 0;">+<span id="LC4254" class="line" lang="c"> <span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">align_residual</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">exon_residual</span><span class="p">)</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">align_residual</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">exon_residual</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4255" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4255
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<pre style="margin: 0;">+<span id="LC4255" class="line" lang="c"> <span class="n" style="color: #333;">querystart</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">queryend</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">len</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/* tminus */</span></span>
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4256
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<pre style="margin: 0;">+<span id="LC4256" class="line" lang="c"> </span>
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<td class="diff-line-num new new_line" data-linenumber="4257" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4257
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<pre style="margin: 0;">+<span id="LC4257" class="line" lang="c"> <span class="n" style="color: #333;">alignend</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">chroffset</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">genomicpos</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4258" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4258
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<pre style="margin: 0;">+<span id="LC4258" class="line" lang="c"> <span class="n" style="color: #333;">alignstart</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alignend</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">len</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/* gplus */</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4259" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4259
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<pre style="margin: 0;">+<span id="LC4259" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">left</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alignend</span> <span class="o" style="font-weight: 600;">-</span> <span class="p">(</span><span class="n" style="color: #333;">querylength</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">queryend</span><span class="p">));</span> <span class="cm" style="color: #998; font-style: italic;">/* tminus != gplus */</span></span>
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4260
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<pre style="margin: 0;">+<span id="LC4260" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"tr ultrafast gap case 3 1st part query %d..%d, align %u..%u [%u..%u], left %u = %u - (%d - %d)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span></span>
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4261
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<pre style="margin: 0;">+<span id="LC4261" class="line" lang="c"> <span class="n" style="color: #333;">querystart</span><span class="p">,</span><span class="n" style="color: #333;">queryend</span><span class="p">,</span><span class="n" style="color: #333;">alignstart</span><span class="p">,</span><span class="n" style="color: #333;">alignend</span><span class="p">,</span><span class="n" style="color: #333;">alignstart</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">chroffset</span><span class="p">,</span><span class="n" style="color: #333;">alignend</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">chroffset</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4262" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4262
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<pre style="margin: 0;">+<span id="LC4262" class="line" lang="c"> <span class="n" style="color: #333;">left</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">chroffset</span><span class="p">,</span><span class="n" style="color: #333;">alignend</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">chroffset</span><span class="p">,</span><span class="n" style="color: #333;">querylength</span><span class="p">,</span><span class="n" style="color: #333;">queryend</span><span class="p">));</span></span>
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4263
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<pre style="margin: 0;">+<span id="LC4263" class="line" lang="c"> </span>
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<td class="diff-line-num new new_line" data-linenumber="4264" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4264
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<pre style="margin: 0;">+<span id="LC4264" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* tminus: plus alignend first */</span></span>
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4265
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<pre style="margin: 0;">+<span id="LC4265" class="line" lang="c"> <span class="n" style="color: #333;">endpoints</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Uintlist_push</span><span class="p">(</span><span class="n" style="color: #333;">endpoints</span><span class="p">,(</span><span class="n" style="color: #333;">Chrpos_T</span><span class="p">)</span> <span class="p">(</span><span class="n" style="color: #333;">alignend</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">chroffset</span><span class="p">));</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4266" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4266
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<pre style="margin: 0;">+<span id="LC4266" class="line" lang="c"> <span class="n" style="color: #333;">endpoints</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Uintlist_push</span><span class="p">(</span><span class="n" style="color: #333;">endpoints</span><span class="p">,(</span><span class="n" style="color: #333;">Chrpos_T</span><span class="p">)</span> <span class="p">(</span><span class="n" style="color: #333;">alignstart</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">chroffset</span><span class="p">));</span></span>
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4267
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<pre style="margin: 0;">+<span id="LC4267" class="line" lang="c"> </span>
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<td class="diff-line-num new new_line" data-linenumber="4268" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4268
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<pre style="margin: 0;">+<span id="LC4268" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">align_residual</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">exon_residual</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4269" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4269
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<pre style="margin: 0;">+<span id="LC4269" class="line" lang="c"> <span class="n" style="color: #333;">exon_residual</span> <span class="o" style="font-weight: 600;">-=</span> <span class="n" style="color: #333;">align_residual</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/* Need to know this if we have a following deletion */</span></span>
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4270
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<pre style="margin: 0;">+<span id="LC4270" class="line" lang="c"> <span class="n" style="color: #333;">align_residual</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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4271
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<pre style="margin: 0;">+<span id="LC4271" class="line" lang="c"> <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="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">exoni</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">nexons</span><span class="p">)</span> <span class="p">{</span></span>
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4272
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<pre style="margin: 0;">+<span id="LC4272" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Aligning past the end of the transcript */</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4273" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4273
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<pre style="margin: 0;">+<span id="LC4273" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"6 ABORTING BECAUSE ALIGNING PAST END OF TRANSCRIPT</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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4274
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<pre style="margin: 0;">+<span id="LC4274" class="line" lang="c"> <span class="n" style="color: #333;">align_residual</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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4281
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4275
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<pre style="margin: 0;"> <span id="LC4275" class="line" lang="c"> <span class="n" style="color: #333;">abortp</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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4282
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<td class="diff-line-num new_line" data-linenumber="4276" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4276
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<pre style="margin: 0;"> <span id="LC4276" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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4283
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<td class="diff-line-num new_line old" data-linenumber="4277" 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="LC4283" class="line" lang="c"> <span class="n" style="color: #333;">gaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Intlist_push</span><span class="p">(</span><span class="n" style="color: #333;">gaps</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;">adj</span><span class="p">);</span></span>
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4277
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<pre style="margin: 0;">+<span id="LC4277" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* nintrons += 1; */</span></span>
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4278
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<pre style="margin: 0;">+<span id="LC4278" class="line" lang="c"> <span class="n" style="color: #333;">align_residual</span> <span class="o" style="font-weight: 600;">-=</span> <span class="n" style="color: #333;">len</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4279" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4279
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<pre style="margin: 0;">+<span id="LC4279" class="line" lang="c"> <span class="n" style="color: #333;">queryend</span> <span class="o" style="font-weight: 600;">-=</span> <span class="n" style="color: #333;">len</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/* tminus */</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4280" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4280
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<pre style="margin: 0;">+<span id="LC4280" class="line" lang="c"> <span class="n" style="color: #333;">genomicpos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">exonstarts</span><span class="p">[</span><span class="n" style="color: #333;">exoni</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="cm" style="color: #998; font-style: italic;">/* gplus */</span></span>
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4281
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<pre style="margin: 0;">+<span id="LC4281" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"genomicpos %u = %u - 1</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">genomicpos</span><span class="p">,</span><span class="n" style="color: #333;">exonstarts</span><span class="p">[</span><span class="n" style="color: #333;">exoni</span><span class="p">]));</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4282" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4282
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<pre style="margin: 0;">+<span id="LC4282" class="line" lang="c"> <span class="n" style="color: #333;">exon_residual</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">exonbounds</span><span class="p">[</span><span class="n" style="color: #333;">exoni</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">exonbounds</span><span class="p">[</span><span class="n" style="color: #333;">exoni</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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4283
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<pre style="margin: 0;">+<span id="LC4283" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"INTRON</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">));</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4284" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4284
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<pre style="margin: 0;">+<span id="LC4284" class="line" lang="c"> <span class="n" style="color: #333;">gaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Intlist_push</span><span class="p">(</span><span class="n" style="color: #333;">gaps</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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4284
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4285
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<pre style="margin: 0;"> <span id="LC4285" class="line" lang="c"> <span class="p">}</span></span>
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4285
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<pre style="margin: 0;">-<span id="LC4285" class="line" lang="c"></span>
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4286
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<td class="diff-line-num new_line old" data-linenumber="4286" 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="LC4286" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* second part */</span></span>
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4287
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<td class="diff-line-num new_line old" data-linenumber="4286" 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="LC4287" class="line" lang="c"> <span class="n" style="color: #333;">tr_left</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tr_left1</span><span class="p">;</span></span>
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4288
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<td class="diff-line-num new_line old" data-linenumber="4286" 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="LC4288" class="line" lang="c"> <span class="n" style="color: #333;">queryend</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">querylength</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">indel_pos</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">ninserts</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/* tminus: compute from queryend to querystart */</span></span>
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4289
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<pre style="margin: 0;">-<span id="LC4289" class="line" lang="c"> <span class="n" style="color: #333;">querystart</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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4290
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<pre style="margin: 0;">-<span id="LC4290" class="line" lang="c"></span>
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4291
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<pre style="margin: 0;">-<span id="LC4291" class="line" lang="c"> <span class="n" style="color: #333;">trstart</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">transcript_diag1</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="n" style="color: #333;">querylength</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">queryend</span><span class="p">);</span> <span class="cm" style="color: #998; font-style: italic;">/* tminus */</span></span>
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4292
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<td class="diff-line-num new_line old" data-linenumber="4286" 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="LC4292" class="line" lang="c"> <span class="n" style="color: #333;">overall_trend</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">transcript_diag1</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="n" style="color: #333;">querylength</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">querystart</span><span class="p">);</span> <span class="cm" style="color: #998; font-style: italic;">/* tminus */</span></span>
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4293
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<pre style="margin: 0;">-<span id="LC4293" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"transcript_diag %d, trstart %d, trend %d, tr_left %u</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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4294
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<pre style="margin: 0;">-<span id="LC4294" class="line" lang="c"> <span class="n" style="color: #333;">transcript_diag1</span><span class="p">,</span><span class="n" style="color: #333;">trstart</span><span class="p">,</span><span class="n" style="color: #333;">overall_trend</span><span class="p">,</span><span class="n" style="color: #333;">tr_left</span><span class="p">));</span></span>
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4286
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<pre style="margin: 0;">+<span id="LC4286" class="line" lang="c"> <span class="p">}</span></span>
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4287
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<pre style="margin: 0;">+<span id="LC4287" class="line" lang="c"> <span class="p">}</span></span>
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4295
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4288
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<pre style="margin: 0;"> <span id="LC4288" class="line" lang="c"> </span>
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4296
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<pre style="margin: 0;">-<span id="LC4296" class="line" lang="c"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">exoni</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">nexons</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">exonbounds</span><span class="p">[</span><span class="n" style="color: #333;">exoni</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">trstart</span><span class="p">)</span> <span class="p">{</span></span>
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4297
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<pre style="margin: 0;">-<span id="LC4297" class="line" lang="c"> <span class="n" style="color: #333;">exoni</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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4298
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<pre style="margin: 0;">-<span id="LC4298" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4289" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4289
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<pre style="margin: 0;">+<span id="LC4289" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* gap */</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4290" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4290
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<pre style="margin: 0;">+<span id="LC4290" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"INDEL: last piece %d | nindels %d | next piece %d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">len</span><span class="p">,</span><span class="n" style="color: #333;">nindels</span><span class="p">,</span><span class="n" style="color: #333;">exon_residual</span><span class="p">));</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4291" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4291
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<pre style="margin: 0;">+<span id="LC4291" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"exon residual %d vs nindels %d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">exon_residual</span><span class="p">,</span><span class="n" style="color: #333;">nindels</span><span class="p">));</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4292" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4292
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<pre style="margin: 0;">+<span id="LC4292" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">abortp</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4293" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4293
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<pre style="margin: 0;">+<span id="LC4293" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Skip */</span></span>
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4294
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<pre style="margin: 0;">+<span id="LC4294" class="line" lang="c"> <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="cm" style="color: #998; font-style: italic;">/*len <= nindels ||*/</span><span class="n" style="color: #333;">exon_residual</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">nindels</span><span class="p">)</span> <span class="p">{</span></span>
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4295
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<pre style="margin: 0;">+<span id="LC4295" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"ABORTING BECAUSE INDEL OVERLAPS SPLICE SITE (7)</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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4296
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<pre style="margin: 0;">+<span id="LC4296" class="line" lang="c"> <span class="n" style="color: #333;">abortp</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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4297
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<pre style="margin: 0;">+<span id="LC4297" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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4298
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<pre style="margin: 0;">+<span id="LC4298" class="line" lang="c"> <span class="n" style="color: #333;">gaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Intlist_push</span><span class="p">(</span><span class="n" style="color: #333;">gaps</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;">adj</span><span class="p">);</span></span>
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4299
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<pre style="margin: 0;">+<span id="LC4299" class="line" lang="c"> <span class="p">}</span></span>
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4299
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4300
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<pre style="margin: 0;"> <span id="LC4300" class="line" lang="c"> </span>
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4300
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<td class="diff-line-num new_line old" data-linenumber="4301" 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="LC4300" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">exoni</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">nexons</span><span class="p">)</span> <span class="p">{</span></span>
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4301
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<td class="diff-line-num new_line old" data-linenumber="4301" 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="LC4301" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"ABORTING BECAUSE OF EXONI %d >= NEXONS %d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">exoni</span><span class="p">,</span><span class="n" style="color: #333;">nexons</span><span class="p">));</span></span>
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4301
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<pre style="margin: 0;">+<span id="LC4301" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* second part */</span></span>
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4302
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<pre style="margin: 0;">+<span id="LC4302" class="line" lang="c"> <span class="n" style="color: #333;">tr_left</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tr_left1</span><span class="p">;</span></span>
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4303
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<pre style="margin: 0;">+<span id="LC4303" class="line" lang="c"> <span class="n" style="color: #333;">queryend</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">querylength</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">indel_pos</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">ninserts</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/* tminus: compute from queryend to querystart */</span></span>
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4304
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<pre style="margin: 0;">+<span id="LC4304" class="line" lang="c"> <span class="n" style="color: #333;">querystart</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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4305
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<pre style="margin: 0;">+<span id="LC4305" class="line" lang="c"> </span>
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<td class="diff-line-num new new_line" data-linenumber="4306" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4306
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<pre style="margin: 0;">+<span id="LC4306" class="line" lang="c"> <span class="n" style="color: #333;">trstart</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">transcript_diag1</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="n" style="color: #333;">querylength</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">queryend</span><span class="p">);</span> <span class="cm" style="color: #998; font-style: italic;">/* tminus */</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4307" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4307
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<pre style="margin: 0;">+<span id="LC4307" class="line" lang="c"> <span class="n" style="color: #333;">overall_trend</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">transcript_diag1</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="n" style="color: #333;">querylength</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">querystart</span><span class="p">);</span> <span class="cm" style="color: #998; font-style: italic;">/* tminus */</span></span>
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<td class="diff-line-num new old_line" data-linenumber="4302" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="4308" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4308
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<pre style="margin: 0;">+<span id="LC4308" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"transcript_diag %d, trstart %d, trend %d, tr_left %u</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span></span>
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<td class="diff-line-num new old_line" data-linenumber="4302" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="4309" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4309
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<pre style="margin: 0;">+<span id="LC4309" class="line" lang="c"> <span class="n" style="color: #333;">transcript_diag1</span><span class="p">,</span><span class="n" style="color: #333;">trstart</span><span class="p">,</span><span class="n" style="color: #333;">overall_trend</span><span class="p">,</span><span class="n" style="color: #333;">tr_left</span><span class="p">));</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4310" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4310
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<pre style="margin: 0;">+<span id="LC4310" class="line" lang="c"> </span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="4302" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="4311" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4311
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<pre style="margin: 0;">+<span id="LC4311" class="line" lang="c"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">exoni</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">nexons</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">exonbounds</span><span class="p">[</span><span class="n" style="color: #333;">exoni</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">trstart</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4312" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4312
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<pre style="margin: 0;">+<span id="LC4312" class="line" lang="c"> <span class="n" style="color: #333;">exoni</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4313" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4313
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<pre style="margin: 0;">+<span id="LC4313" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num new old_line" data-linenumber="4302" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="4314" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4314
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<pre style="margin: 0;">+<span id="LC4314" class="line" lang="c"> </span>
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<td class="diff-line-num new new_line" data-linenumber="4315" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4315
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<pre style="margin: 0;">+<span id="LC4315" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">exoni</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">nexons</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4316" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4316
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<pre style="margin: 0;">+<span id="LC4316" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"ABORTING BECAUSE OF EXONI %d >= NEXONS %d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">exoni</span><span class="p">,</span><span class="n" style="color: #333;">nexons</span><span class="p">));</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4317" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4317
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<pre style="margin: 0;">+<span id="LC4317" class="line" lang="c"> <span class="n" style="color: #333;">abortp</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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<td class="diff-line-num new old_line" data-linenumber="4302" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="4318" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4318
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<pre style="margin: 0;">+<span id="LC4318" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="diff-line-num new old_line" data-linenumber="4302" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="4319" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4319
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<pre style="margin: 0;">+<span id="LC4319" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"(14) exoni %d out of nexons %d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">exoni</span><span class="p">,</span><span class="n" style="color: #333;">nexons</span><span class="p">));</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4320" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4320
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<pre style="margin: 0;">+<span id="LC4320" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">exoni</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>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="4321" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4321
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<pre style="margin: 0;">+<span id="LC4321" class="line" lang="c"> <span class="n" style="color: #333;">exonpos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">trstart</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4322" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4322
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<pre style="margin: 0;">+<span id="LC4322" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4323" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4323
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<pre style="margin: 0;">+<span id="LC4323" class="line" lang="c"> <span class="n" style="color: #333;">exonpos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">trstart</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">exonbounds</span><span class="p">[</span><span class="n" style="color: #333;">exoni</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">];</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4324" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4324
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<pre style="margin: 0;">+<span id="LC4324" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4325" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4325
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<pre style="margin: 0;">+<span id="LC4325" class="line" lang="c"> <span class="n" style="color: #333;">exon_residual</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">exonbounds</span><span class="p">[</span><span class="n" style="color: #333;">exoni</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">trstart</span><span class="p">;</span></span>
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4326
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<pre style="margin: 0;">+<span id="LC4326" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"exoni %d => exon_residual %d, exonpos %d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">exoni</span><span class="p">,</span><span class="n" style="color: #333;">exon_residual</span><span class="p">,</span><span class="n" style="color: #333;">exonpos</span><span class="p">));</span></span>
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4327
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<pre style="margin: 0;">+<span id="LC4327" class="line" lang="c"> </span>
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<td class="diff-line-num new new_line" data-linenumber="4328" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4328
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<pre style="margin: 0;">+<span id="LC4328" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Generate one substring per exon */</span></span>
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4329
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<pre style="margin: 0;">+<span id="LC4329" class="line" lang="c"> <span class="n" style="color: #333;">genomicpos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">exonstarts</span><span class="p">[</span><span class="n" style="color: #333;">exoni</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">exonpos</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/* gplus */</span></span>
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4330
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<pre style="margin: 0;">+<span id="LC4330" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"genomicpos %u = %u + %u - 1</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">genomicpos</span><span class="p">,</span><span class="n" style="color: #333;">exonstarts</span><span class="p">[</span><span class="n" style="color: #333;">exoni</span><span class="p">],</span><span class="n" style="color: #333;">exonpos</span><span class="p">));</span></span>
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4331
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<pre style="margin: 0;">+<span id="LC4331" class="line" lang="c"> <span class="n" style="color: #333;">align_residual</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">queryend</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">querystart</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4332" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4332
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<pre style="margin: 0;">+<span id="LC4332" class="line" lang="c"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">align_residual</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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4333
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<pre style="margin: 0;">+<span id="LC4333" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"abortp %d,align_residual %d, exon_residual %d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">abortp</span><span class="p">,</span><span class="n" style="color: #333;">align_residual</span><span class="p">,</span><span class="n" style="color: #333;">exon_residual</span><span class="p">));</span></span>
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4334
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<pre style="margin: 0;">+<span id="LC4334" class="line" lang="c"> <span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">align_residual</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">exon_residual</span><span class="p">)</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">align_residual</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">exon_residual</span><span class="p">;</span></span>
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4335
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<pre style="margin: 0;">+<span id="LC4335" class="line" lang="c"> <span class="n" style="color: #333;">querystart</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">queryend</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">len</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/* tminus */</span></span>
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4336
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<pre style="margin: 0;">+<span id="LC4336" class="line" lang="c"> </span>
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4337
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<pre style="margin: 0;">+<span id="LC4337" class="line" lang="c"> <span class="n" style="color: #333;">alignend</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">chroffset</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">genomicpos</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4338" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4338
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<pre style="margin: 0;">+<span id="LC4338" class="line" lang="c"> <span class="n" style="color: #333;">alignstart</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alignend</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">len</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/* gplus */</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4339" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4339
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<pre style="margin: 0;">+<span id="LC4339" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">left</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alignend</span> <span class="o" style="font-weight: 600;">-</span> <span class="p">(</span><span class="n" style="color: #333;">querylength</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">queryend</span><span class="p">));</span> <span class="cm" style="color: #998; font-style: italic;">/* tminus != gplus */</span></span>
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4340
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<pre style="margin: 0;">+<span id="LC4340" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"tr ultrafast gap case 3 2nd part query %d..%d, align %u..%u [%u..%u], left %u = %u - (%d - %d)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span></span>
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4341
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<pre style="margin: 0;">+<span id="LC4341" class="line" lang="c"> <span class="n" style="color: #333;">querystart</span><span class="p">,</span><span class="n" style="color: #333;">queryend</span><span class="p">,</span><span class="n" style="color: #333;">alignstart</span><span class="p">,</span><span class="n" style="color: #333;">alignend</span><span class="p">,</span><span class="n" style="color: #333;">alignstart</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">chroffset</span><span class="p">,</span><span class="n" style="color: #333;">alignend</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">chroffset</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4342" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4342
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<pre style="margin: 0;">+<span id="LC4342" class="line" lang="c"> <span class="n" style="color: #333;">left</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">chroffset</span><span class="p">,</span><span class="n" style="color: #333;">alignend</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">chroffset</span><span class="p">,</span><span class="n" style="color: #333;">querylength</span><span class="p">,</span><span class="n" style="color: #333;">queryend</span><span class="p">));</span></span>
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4343
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<pre style="margin: 0;">+<span id="LC4343" class="line" lang="c"> </span>
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4344
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<pre style="margin: 0;">+<span id="LC4344" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* tminus: plus alignend first */</span></span>
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4345
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<pre style="margin: 0;">+<span id="LC4345" class="line" lang="c"> <span class="n" style="color: #333;">endpoints</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Uintlist_push</span><span class="p">(</span><span class="n" style="color: #333;">endpoints</span><span class="p">,(</span><span class="n" style="color: #333;">Chrpos_T</span><span class="p">)</span> <span class="p">(</span><span class="n" style="color: #333;">alignend</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">chroffset</span><span class="p">));</span></span>
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4346
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<pre style="margin: 0;">+<span id="LC4346" class="line" lang="c"> <span class="n" style="color: #333;">endpoints</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Uintlist_push</span><span class="p">(</span><span class="n" style="color: #333;">endpoints</span><span class="p">,(</span><span class="n" style="color: #333;">Chrpos_T</span><span class="p">)</span> <span class="p">(</span><span class="n" style="color: #333;">alignstart</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">chroffset</span><span class="p">));</span></span>
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4347
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<pre style="margin: 0;">+<span id="LC4347" class="line" lang="c"> </span>
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4348
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<pre style="margin: 0;">+<span id="LC4348" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">align_residual</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">exon_residual</span><span class="p">)</span> <span class="p">{</span></span>
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4349
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<pre style="margin: 0;">+<span id="LC4349" class="line" lang="c"> <span class="n" style="color: #333;">exon_residual</span> <span class="o" style="font-weight: 600;">-=</span> <span class="n" style="color: #333;">align_residual</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/* Need to know this if we have a following deletion */</span></span>
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4350
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<pre style="margin: 0;">+<span id="LC4350" class="line" lang="c"> <span class="n" style="color: #333;">align_residual</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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4351
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<pre style="margin: 0;">+<span id="LC4351" class="line" lang="c"> <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="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">exoni</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">nexons</span><span class="p">)</span> <span class="p">{</span></span>
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4352
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<pre style="margin: 0;">+<span id="LC4352" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Aligning past the end of the transcript */</span></span>
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4353
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<pre style="margin: 0;">+<span id="LC4353" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"6 ABORTING BECAUSE ALIGNING PAST END OF TRANSCRIPT</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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4354
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<pre style="margin: 0;">+<span id="LC4354" class="line" lang="c"> <span class="n" style="color: #333;">align_residual</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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4302
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4355
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<pre style="margin: 0;"> <span id="LC4355" class="line" lang="c"> <span class="n" style="color: #333;">abortp</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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4303
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4356
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<pre style="margin: 0;"> <span id="LC4356" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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4304
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<pre style="margin: 0;">-<span id="LC4304" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"(14) exoni %d out of nexons %d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">exoni</span><span class="p">,</span><span class="n" style="color: #333;">nexons</span><span class="p">));</span></span>
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4305
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<pre style="margin: 0;">-<span id="LC4305" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">exoni</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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4306
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<pre style="margin: 0;">-<span id="LC4306" class="line" lang="c"> <span class="n" style="color: #333;">exonpos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">trstart</span><span class="p">;</span></span>
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4307
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<pre style="margin: 0;">-<span id="LC4307" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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4308
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<pre style="margin: 0;">-<span id="LC4308" class="line" lang="c"> <span class="n" style="color: #333;">exonpos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">trstart</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">exonbounds</span><span class="p">[</span><span class="n" style="color: #333;">exoni</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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4309
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<pre style="margin: 0;">-<span id="LC4309" class="line" lang="c"> <span class="p">}</span></span>
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4310
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<pre style="margin: 0;">-<span id="LC4310" class="line" lang="c"> <span class="n" style="color: #333;">exon_residual</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">exonbounds</span><span class="p">[</span><span class="n" style="color: #333;">exoni</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">trstart</span><span class="p">;</span></span>
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4311
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<pre style="margin: 0;">-<span id="LC4311" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"exoni %d => exon_residual %d, exonpos %d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">exoni</span><span class="p">,</span><span class="n" style="color: #333;">exon_residual</span><span class="p">,</span><span class="n" style="color: #333;">exonpos</span><span class="p">));</span></span>
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4312
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<td class="diff-line-num new_line old" data-linenumber="4357" 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="LC4312" class="line" lang="c"></span>
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<td class="diff-line-num old old_line" data-linenumber="4313" 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">
4313
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<td class="diff-line-num new_line old" data-linenumber="4357" 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="LC4313" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Generate one substring per exon */</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4314" 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">
4314
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<td class="diff-line-num new_line old" data-linenumber="4357" 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="LC4314" class="line" lang="c"> <span class="n" style="color: #333;">genomicpos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">exonstarts</span><span class="p">[</span><span class="n" style="color: #333;">exoni</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">exonpos</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/* gplus */</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4315" 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">
4315
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<td class="diff-line-num new_line old" data-linenumber="4357" 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="LC4315" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"genomicpos %u = %u + %u - 1</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">genomicpos</span><span class="p">,</span><span class="n" style="color: #333;">exonstarts</span><span class="p">[</span><span class="n" style="color: #333;">exoni</span><span class="p">],</span><span class="n" style="color: #333;">exonpos</span><span class="p">));</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4316" 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">
4316
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<td class="diff-line-num new_line old" data-linenumber="4357" 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="LC4316" class="line" lang="c"> <span class="n" style="color: #333;">align_residual</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">queryend</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">querystart</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4317" 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">
4317
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<td class="diff-line-num new_line old" data-linenumber="4357" 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="LC4317" class="line" lang="c"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">align_residual</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4318" 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">
4318
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<td class="diff-line-num new_line old" data-linenumber="4357" 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="LC4318" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"abortp %d,align_residual %d, exon_residual %d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">abortp</span><span class="p">,</span><span class="n" style="color: #333;">align_residual</span><span class="p">,</span><span class="n" style="color: #333;">exon_residual</span><span class="p">));</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4319" 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">
4319
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<td class="diff-line-num new_line old" data-linenumber="4357" 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="LC4319" class="line" lang="c"> <span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">align_residual</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">exon_residual</span><span class="p">)</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">align_residual</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">exon_residual</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4320" 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">
4320
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<td class="diff-line-num new_line old" data-linenumber="4357" 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="LC4320" class="line" lang="c"> <span class="n" style="color: #333;">querystart</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">queryend</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">len</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/* tminus */</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4321" 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">
4321
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<td class="diff-line-num new_line old" data-linenumber="4357" 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="LC4321" class="line" lang="c"> </span>
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<td class="diff-line-num old old_line" data-linenumber="4322" 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">
4322
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<td class="diff-line-num new_line old" data-linenumber="4357" 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="LC4322" class="line" lang="c"> <span class="n" style="color: #333;">alignend</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">chroffset</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">genomicpos</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4323" 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">
4323
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<td class="diff-line-num new_line old" data-linenumber="4357" 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="LC4323" class="line" lang="c"> <span class="n" style="color: #333;">alignstart</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alignend</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">len</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/* gplus */</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4324" 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">
4324
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<td class="diff-line-num new_line old" data-linenumber="4357" 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="LC4324" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">left</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alignend</span> <span class="o" style="font-weight: 600;">-</span> <span class="p">(</span><span class="n" style="color: #333;">querylength</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">queryend</span><span class="p">));</span> <span class="cm" style="color: #998; font-style: italic;">/* tminus != gplus */</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4325" 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">
4325
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<td class="diff-line-num new_line old" data-linenumber="4357" 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="LC4325" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"tr ultrafast gap case 3 2nd part query %d..%d, align %u..%u [%u..%u], left %u = %u - (%d - %d)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4326" 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">
4326
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<td class="diff-line-num new_line old" data-linenumber="4357" 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="LC4326" class="line" lang="c"> <span class="n" style="color: #333;">querystart</span><span class="p">,</span><span class="n" style="color: #333;">queryend</span><span class="p">,</span><span class="n" style="color: #333;">alignstart</span><span class="p">,</span><span class="n" style="color: #333;">alignend</span><span class="p">,</span><span class="n" style="color: #333;">alignstart</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">chroffset</span><span class="p">,</span><span class="n" style="color: #333;">alignend</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">chroffset</span><span class="p">,</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4327" 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">
4327
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<td class="diff-line-num new_line old" data-linenumber="4357" 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="LC4327" class="line" lang="c"> <span class="n" style="color: #333;">left</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">chroffset</span><span class="p">,</span><span class="n" style="color: #333;">alignend</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">chroffset</span><span class="p">,</span><span class="n" style="color: #333;">querylength</span><span class="p">,</span><span class="n" style="color: #333;">queryend</span><span class="p">));</span></span>
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4328
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<pre style="margin: 0;">-<span id="LC4328" class="line" lang="c"></span>
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<td class="diff-line-num old old_line" data-linenumber="4329" 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">
4329
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<td class="diff-line-num new_line old" data-linenumber="4357" 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="LC4329" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* tminus: plus alignend first */</span></span>
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4330
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<pre style="margin: 0;">-<span id="LC4330" class="line" lang="c"> <span class="n" style="color: #333;">endpoints</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Uintlist_push</span><span class="p">(</span><span class="n" style="color: #333;">endpoints</span><span class="p">,(</span><span class="n" style="color: #333;">Chrpos_T</span><span class="p">)</span> <span class="p">(</span><span class="n" style="color: #333;">alignend</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">chroffset</span><span class="p">));</span></span>
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4331
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<pre style="margin: 0;">-<span id="LC4331" class="line" lang="c"> <span class="n" style="color: #333;">endpoints</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Uintlist_push</span><span class="p">(</span><span class="n" style="color: #333;">endpoints</span><span class="p">,(</span><span class="n" style="color: #333;">Chrpos_T</span><span class="p">)</span> <span class="p">(</span><span class="n" style="color: #333;">alignstart</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">chroffset</span><span class="p">));</span></span>
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4332
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<pre style="margin: 0;">-<span id="LC4332" class="line" lang="c"></span>
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4333
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<td class="diff-line-num new_line old" data-linenumber="4357" 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="LC4333" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">align_residual</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">exon_residual</span><span class="p">)</span> <span class="p">{</span></span>
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4334
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<td class="diff-line-num new_line old" data-linenumber="4357" 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="LC4334" class="line" lang="c"> <span class="n" style="color: #333;">exon_residual</span> <span class="o" style="font-weight: 600;">-=</span> <span class="n" style="color: #333;">align_residual</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/* Need to know this if we have a following deletion */</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4335" 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">
4335
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<td class="diff-line-num new_line old" data-linenumber="4357" 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="LC4335" class="line" lang="c"> <span class="n" style="color: #333;">align_residual</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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4336
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<pre style="margin: 0;">-<span id="LC4336" class="line" lang="c"> <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="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">exoni</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">nexons</span><span class="p">)</span> <span class="p">{</span></span>
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4337
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<td class="diff-line-num new_line old" data-linenumber="4357" 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="LC4337" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Aligning past the end of the transcript */</span></span>
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4338
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<td class="diff-line-num new_line old" data-linenumber="4357" 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="LC4338" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"6 ABORTING BECAUSE ALIGNING PAST END OF TRANSCRIPT</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">));</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4339" 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">
4339
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<td class="diff-line-num new_line old" data-linenumber="4357" 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="LC4339" class="line" lang="c"> <span class="n" style="color: #333;">align_residual</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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4340
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<pre style="margin: 0;">-<span id="LC4340" class="line" lang="c"> <span class="n" style="color: #333;">abortp</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4341" 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">
4341
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<pre style="margin: 0;">-<span id="LC4341" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4342" 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">
4342
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<td class="diff-line-num new_line old" data-linenumber="4357" 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="LC4342" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* nintrons += 1; */</span></span>
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4343
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<td class="diff-line-num new_line old" data-linenumber="4357" 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="LC4343" class="line" lang="c"> <span class="n" style="color: #333;">align_residual</span> <span class="o" style="font-weight: 600;">-=</span> <span class="n" style="color: #333;">len</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4344" 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">
4344
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<td class="diff-line-num new_line old" data-linenumber="4357" 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="LC4344" class="line" lang="c"> <span class="n" style="color: #333;">queryend</span> <span class="o" style="font-weight: 600;">-=</span> <span class="n" style="color: #333;">len</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/* tminus */</span></span>
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4345
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<pre style="margin: 0;">-<span id="LC4345" class="line" lang="c"> <span class="n" style="color: #333;">genomicpos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">exonstarts</span><span class="p">[</span><span class="n" style="color: #333;">exoni</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="cm" style="color: #998; font-style: italic;">/* gplus */</span></span>
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4346
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<td class="diff-line-num new_line old" data-linenumber="4357" 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="LC4346" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"genomicpos %u = %u - 1</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">genomicpos</span><span class="p">,</span><span class="n" style="color: #333;">exonstarts</span><span class="p">[</span><span class="n" style="color: #333;">exoni</span><span class="p">]));</span></span>
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4347
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<td class="diff-line-num new_line old" data-linenumber="4357" 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="LC4347" class="line" lang="c"> <span class="n" style="color: #333;">exon_residual</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">exonbounds</span><span class="p">[</span><span class="n" style="color: #333;">exoni</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">exonbounds</span><span class="p">[</span><span class="n" style="color: #333;">exoni</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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4348
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<pre style="margin: 0;">-<span id="LC4348" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"INTRON</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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4349
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<pre style="margin: 0;">-<span id="LC4349" class="line" lang="c"> <span class="n" style="color: #333;">gaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Intlist_push</span><span class="p">(</span><span class="n" style="color: #333;">gaps</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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4350
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<pre style="margin: 0;">-<span id="LC4350" class="line" lang="c"> <span class="p">}</span></span>
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4351
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<pre style="margin: 0;">-<span id="LC4351" class="line" lang="c"> <span class="p">}</span></span>
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4352
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<pre style="margin: 0;">-<span id="LC4352" class="line" lang="c"> <span class="p">}</span></span>
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4353
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<pre style="margin: 0;">-<span id="LC4353" class="line" lang="c"></span>
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4354
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<pre style="margin: 0;">-<span id="LC4354" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">abortp</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">)</span> <span class="p">{</span></span>
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4355
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<pre style="margin: 0;">-<span id="LC4355" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"ABORTING PATH</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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4356
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<pre style="margin: 0;">-<span id="LC4356" class="line" lang="c"> <span class="n" style="color: #333;">Uintlist_free</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">endpoints</span><span class="p">);</span></span>
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4357
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<pre style="margin: 0;">-<span id="LC4357" class="line" lang="c"> <span class="n" style="color: #333;">Intlist_free</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">gaps</span><span class="p">);</span></span>
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4358
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<pre style="margin: 0;">-<span id="LC4358" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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4359
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<pre style="margin: 0;">-<span id="LC4359" class="line" lang="c"> <span class="n" style="color: #333;">endpoints</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Uintlist_reverse</span><span class="p">(</span><span class="n" style="color: #333;">endpoints</span><span class="p">);</span> <span class="cm" style="color: #998; font-style: italic;">/* gplus */</span></span>
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4360
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<pre style="margin: 0;">-<span id="LC4360" class="line" lang="c"> <span class="n" style="color: #333;">gaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Intlist_reverse</span><span class="p">(</span><span class="n" style="color: #333;">gaps</span><span class="p">);</span> <span class="cm" style="color: #998; font-style: italic;">/* gplus */</span></span>
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4361
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<pre style="margin: 0;">-<span id="LC4361" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"MINUS PATH %d. ENDPOINTS: %s. GAPS: %s</span><span class="se" style="color: #d14;">\n\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span></span>
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4362
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<pre style="margin: 0;">-<span id="LC4362" class="line" lang="c"> <span class="n" style="color: #333;">ngminus</span><span class="p">,</span><span class="n" style="color: #333;">Uintlist_to_string</span><span class="p">(</span><span class="n" style="color: #333;">endpoints</span><span class="p">),</span><span class="n" style="color: #333;">Intlist_to_string</span><span class="p">(</span><span class="n" style="color: #333;">gaps</span><span class="p">)));</span></span>
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4363
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<pre style="margin: 0;">-<span id="LC4363" class="line" lang="c"> <span class="n" style="color: #333;">gminus_paths</span><span class="p">[</span><span class="n" style="color: #333;">ngminus</span><span class="o" style="font-weight: 600;">++</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Path_new</span><span class="p">(</span><span class="n" style="color: #333;">total_nmatches</span><span class="p">,</span><span class="n" style="color: #333;">trnum</span><span class="p">,</span><span class="n" style="color: #333;">overall_trend</span><span class="p">,</span><span class="n" style="color: #333;">overall_trstart</span><span class="p">,</span></span>
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4364
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<pre style="margin: 0;">-<span id="LC4364" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/*trim_low*/</span><span class="n" style="color: #333;">trim3</span><span class="p">,</span><span class="cm" style="color: #998; font-style: italic;">/*trim_high*/</span><span class="n" style="color: #333;">trim5</span><span class="p">,</span><span class="n" style="color: #333;">chrnum</span><span class="p">,</span><span class="n" style="color: #333;">chroffset</span><span class="p">,</span><span class="n" style="color: #333;">chrhigh</span><span class="p">,</span><span class="n" style="color: #333;">chrlength</span><span class="p">,</span></span>
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4365
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<pre style="margin: 0;">-<span id="LC4365" class="line" lang="c"> <span class="n" style="color: #333;">endpoints</span><span class="p">,</span><span class="n" style="color: #333;">gaps</span><span class="p">,</span><span class="n" style="color: #333;">concordantp</span><span class="p">);</span></span>
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4357
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<pre style="margin: 0;">+<span id="LC4357" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* nintrons += 1; */</span></span>
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4358
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<pre style="margin: 0;">+<span id="LC4358" class="line" lang="c"> <span class="n" style="color: #333;">align_residual</span> <span class="o" style="font-weight: 600;">-=</span> <span class="n" style="color: #333;">len</span><span class="p">;</span></span>
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4359
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<pre style="margin: 0;">+<span id="LC4359" class="line" lang="c"> <span class="n" style="color: #333;">queryend</span> <span class="o" style="font-weight: 600;">-=</span> <span class="n" style="color: #333;">len</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/* tminus */</span></span>
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4360
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<pre style="margin: 0;">+<span id="LC4360" class="line" lang="c"> <span class="n" style="color: #333;">genomicpos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">exonstarts</span><span class="p">[</span><span class="n" style="color: #333;">exoni</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="cm" style="color: #998; font-style: italic;">/* gplus */</span></span>
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4361
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<pre style="margin: 0;">+<span id="LC4361" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"genomicpos %u = %u - 1</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">genomicpos</span><span class="p">,</span><span class="n" style="color: #333;">exonstarts</span><span class="p">[</span><span class="n" style="color: #333;">exoni</span><span class="p">]));</span></span>
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4362
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<pre style="margin: 0;">+<span id="LC4362" class="line" lang="c"> <span class="n" style="color: #333;">exon_residual</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">exonbounds</span><span class="p">[</span><span class="n" style="color: #333;">exoni</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">exonbounds</span><span class="p">[</span><span class="n" style="color: #333;">exoni</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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4363
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<pre style="margin: 0;">+<span id="LC4363" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"INTRON</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">));</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4364" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4364
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<pre style="margin: 0;">+<span id="LC4364" class="line" lang="c"> <span class="n" style="color: #333;">gaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Intlist_push</span><span class="p">(</span><span class="n" style="color: #333;">gaps</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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4366
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4365
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<pre style="margin: 0;"> <span id="LC4365" class="line" lang="c"> <span class="p">}</span></span>
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4366
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<pre style="margin: 0;">+<span id="LC4366" class="line" lang="c"> <span class="p">}</span></span>
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4367
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<pre style="margin: 0;">+<span id="LC4367" class="line" lang="c"> <span class="p">}</span></span>
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4368
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<pre style="margin: 0;">+<span id="LC4368" class="line" lang="c"> </span>
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4369
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<pre style="margin: 0;">+<span id="LC4369" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">abortp</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">)</span> <span class="p">{</span></span>
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4370
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<pre style="margin: 0;">+<span id="LC4370" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"ABORTING PATH</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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4371
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<pre style="margin: 0;">+<span id="LC4371" class="line" lang="c"> <span class="n" style="color: #333;">Uintlist_free</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">endpoints</span><span class="p">);</span></span>
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4372
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<pre style="margin: 0;">+<span id="LC4372" class="line" lang="c"> <span class="n" style="color: #333;">Intlist_free</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">gaps</span><span class="p">);</span></span>
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4373
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<pre style="margin: 0;">+<span id="LC4373" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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4374
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<pre style="margin: 0;">+<span id="LC4374" class="line" lang="c"> <span class="n" style="color: #333;">endpoints</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Uintlist_reverse</span><span class="p">(</span><span class="n" style="color: #333;">endpoints</span><span class="p">);</span> <span class="cm" style="color: #998; font-style: italic;">/* gplus */</span></span>
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4375
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<pre style="margin: 0;">+<span id="LC4375" class="line" lang="c"> <span class="n" style="color: #333;">gaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Intlist_reverse</span><span class="p">(</span><span class="n" style="color: #333;">gaps</span><span class="p">);</span> <span class="cm" style="color: #998; font-style: italic;">/* gplus */</span></span>
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4376
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<pre style="margin: 0;">+<span id="LC4376" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"MINUS PATH %d. ENDPOINTS: %s. GAPS: %s</span><span class="se" style="color: #d14;">\n\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4377" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4377
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<pre style="margin: 0;">+<span id="LC4377" class="line" lang="c"> <span class="n" style="color: #333;">ngminus</span><span class="p">,</span><span class="n" style="color: #333;">Uintlist_to_string</span><span class="p">(</span><span class="n" style="color: #333;">endpoints</span><span class="p">),</span><span class="n" style="color: #333;">Intlist_to_string</span><span class="p">(</span><span class="n" style="color: #333;">gaps</span><span class="p">)));</span></span>
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4378
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<pre style="margin: 0;">+<span id="LC4378" class="line" lang="c"> <span class="n" style="color: #333;">gminus_paths</span><span class="p">[</span><span class="n" style="color: #333;">ngminus</span><span class="o" style="font-weight: 600;">++</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Path_new</span><span class="p">(</span><span class="n" style="color: #333;">total_nmatches</span><span class="p">,</span><span class="n" style="color: #333;">trnum</span><span class="p">,</span><span class="n" style="color: #333;">overall_trend</span><span class="p">,</span><span class="n" style="color: #333;">overall_trstart</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4379" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4379
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<pre style="margin: 0;">+<span id="LC4379" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/*trim_low*/</span><span class="n" style="color: #333;">trim3</span><span class="p">,</span><span class="cm" style="color: #998; font-style: italic;">/*trim_high*/</span><span class="n" style="color: #333;">trim5</span><span class="p">,</span><span class="n" style="color: #333;">chrnum</span><span class="p">,</span><span class="n" style="color: #333;">chroffset</span><span class="p">,</span><span class="n" style="color: #333;">chrhigh</span><span class="p">,</span><span class="n" style="color: #333;">chrlength</span><span class="p">,</span></span>
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4380
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<pre style="margin: 0;">+<span id="LC4380" class="line" lang="c"> <span class="n" style="color: #333;">endpoints</span><span class="p">,</span><span class="n" style="color: #333;">gaps</span><span class="p">,</span><span class="n" style="color: #333;">concordantp</span><span class="p">);</span></span>
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4381
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<pre style="margin: 0;">+<span id="LC4381" class="line" lang="c"> <span class="p">}</span></span>
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4382
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<pre style="margin: 0;"> <span id="LC4382" class="line" lang="c"></span>
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4368
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<pre style="margin: 0;">-<span id="LC4368" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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4369
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<pre style="margin: 0;">-<span id="LC4369" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Case 4 ultrafast gap: tminus, gminus. transcript_plusp == false && transcript_genestrand < 0 */</span></span>
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4370
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<pre style="margin: 0;">-<span id="LC4370" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"Case 4 ultrafast gap: tminus, gminus</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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4371
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<pre style="margin: 0;">-<span id="LC4371" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* sensedir = SENSE_ANTI; */</span></span>
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4372
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<pre style="margin: 0;">-<span id="LC4372" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* plusp = true; */</span></span>
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4373
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<pre style="margin: 0;">-<span id="LC4373" class="line" lang="c"></span>
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4374
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<pre style="margin: 0;">-<span id="LC4374" class="line" lang="c"> <span class="n" style="color: #333;">endpoints</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">Uintlist_T</span><span class="p">)</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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4375
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<pre style="margin: 0;">-<span id="LC4375" class="line" lang="c"> <span class="n" style="color: #333;">gaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">Intlist_T</span><span class="p">)</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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4376
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<pre style="margin: 0;">-<span id="LC4376" class="line" lang="c"></span>
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4377
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<pre style="margin: 0;">-<span id="LC4377" class="line" lang="c"> <span class="n" style="color: #333;">transcript_diag0</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tr_left0</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">troffset</span><span class="p">;</span></span>
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4378
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<pre style="margin: 0;">-<span id="LC4378" class="line" lang="c"> <span class="n" style="color: #333;">transcript_diag1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tr_left1</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">troffset</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC4383" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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4384
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<pre style="margin: 0;">+<span id="LC4384" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Case 4 ultrafast gap: tminus, gminus. transcript_plusp == false && transcript_genestrand < 0 */</span></span>
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<pre style="margin: 0;">+<span id="LC4385" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"Case 4 ultrafast gap: tminus, gminus</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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4386
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<pre style="margin: 0;">+<span id="LC4386" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* sensedir = SENSE_ANTI; */</span></span>
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<pre style="margin: 0;">+<span id="LC4387" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* plusp = true; */</span></span>
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4388
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<pre style="margin: 0;"> <span id="LC4388" class="line" lang="c"></span>
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4380
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<pre style="margin: 0;">-<span id="LC4380" class="line" lang="c"> <span class="n" style="color: #333;">abortp</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="LC4389" class="line" lang="c"> <span class="n" style="color: #333;">nexons</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Transcriptome_exons</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">exonbounds</span><span class="p">,</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">exonstarts</span><span class="p">,</span><span class="n" style="color: #333;">transcriptome</span><span class="p">,</span><span class="n" style="color: #333;">trnum</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC4390" class="line" lang="c"> <span class="n" style="color: #333;">Univ_IIT_interval_bounds</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">chroffset</span><span class="p">,</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">chrhigh</span><span class="p">,</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">chrlength</span><span class="p">,</span><span class="n" style="color: #333;">chromosome_iit</span><span class="p">,</span><span class="n" style="color: #333;">chrnum</span><span class="p">,</span><span class="n" style="color: #333;">circular_typeint</span><span class="p">);</span></span>
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4381
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4391
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<pre style="margin: 0;"> <span id="LC4391" class="line" lang="c"></span>
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4382
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<pre style="margin: 0;">-<span id="LC4382" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* first part */</span></span>
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4383
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<pre style="margin: 0;">-<span id="LC4383" class="line" lang="c"> <span class="n" style="color: #333;">tr_left</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tr_left0</span><span class="p">;</span></span>
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4384
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<pre style="margin: 0;">-<span id="LC4384" class="line" lang="c"> <span class="n" style="color: #333;">queryend</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">querylength</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/* tminus: compute from queryend to querystart */</span></span>
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4385
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<pre style="margin: 0;">-<span id="LC4385" class="line" lang="c"> <span class="n" style="color: #333;">querystart</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">querylength</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">indel_pos</span><span class="p">;</span></span>
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4386
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<pre style="margin: 0;">-<span id="LC4386" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</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;">Analyzing query %d..%d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">querystart</span><span class="p">,</span><span class="n" style="color: #333;">queryend</span><span class="p">));</span></span>
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4392
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<pre style="margin: 0;">+<span id="LC4392" class="line" lang="c"> <span class="n" style="color: #333;">endpoints</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">Uintlist_T</span><span class="p">)</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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4393
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<pre style="margin: 0;">+<span id="LC4393" class="line" lang="c"> <span class="n" style="color: #333;">gaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">Intlist_T</span><span class="p">)</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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4394
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<pre style="margin: 0;">+<span id="LC4394" class="line" lang="c"> <span class="n" style="color: #333;">abortp</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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4387
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4395
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<pre style="margin: 0;"> <span id="LC4395" class="line" lang="c"></span>
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4388
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<pre style="margin: 0;">-<span id="LC4388" class="line" lang="c"> <span class="n" style="color: #333;">overall_trstart</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">trstart</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">transcript_diag0</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="n" style="color: #333;">querylength</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">queryend</span><span class="p">);</span> <span class="cm" style="color: #998; font-style: italic;">/* tminus */</span></span>
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4396
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<pre style="margin: 0;">+<span id="LC4396" class="line" lang="c"> <span class="n" style="color: #333;">transcript_diag0</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tr_left0</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">troffset</span><span class="p">;</span></span>
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4397
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<pre style="margin: 0;">+<span id="LC4397" class="line" lang="c"> <span class="n" style="color: #333;">transcript_diag1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tr_left1</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">troffset</span><span class="p">;</span></span>
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4398
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<pre style="margin: 0;">+<span id="LC4398" class="line" lang="c"> </span>
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<td class="diff-line-num new new_line" data-linenumber="4399" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4399
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<pre style="margin: 0;">+<span id="LC4399" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* first part */</span></span>
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4400
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<pre style="margin: 0;">+<span id="LC4400" class="line" lang="c"> <span class="n" style="color: #333;">tr_left</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tr_left0</span><span class="p">;</span></span>
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4401
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<pre style="margin: 0;">+<span id="LC4401" class="line" lang="c"> <span class="n" style="color: #333;">queryend</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">querylength</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/* tminus: compute from queryend to querystart */</span></span>
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4402
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<pre style="margin: 0;">+<span id="LC4402" class="line" lang="c"> <span class="n" style="color: #333;">querystart</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">querylength</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">indel_pos</span><span class="p">;</span></span>
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4403
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<pre style="margin: 0;">+<span id="LC4403" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</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;">Analyzing query %d..%d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">querystart</span><span class="p">,</span><span class="n" style="color: #333;">queryend</span><span class="p">));</span></span>
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4404
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<pre style="margin: 0;">+<span id="LC4404" class="line" lang="c"> </span>
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4405
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<pre style="margin: 0;">+<span id="LC4405" class="line" lang="c"> <span class="n" style="color: #333;">overall_trstart</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">trstart</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">transcript_diag0</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="n" style="color: #333;">querylength</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">queryend</span><span class="p">);</span> <span class="cm" style="color: #998; font-style: italic;">/* tminus */</span></span>
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4389
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4406
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<pre style="margin: 0;"> <span id="LC4406" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifdef DEBUG2</span></span>
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4390
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<pre style="margin: 0;">-<span id="LC4390" class="line" lang="c"> <span class="idiff left right"> </span><span class="n" style="color: #333;">trend</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">transcript_diag0</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="n" style="color: #333;">querylength</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">querystart</span><span class="p">);</span> <span class="cm" style="color: #998; font-style: italic;">/* tminus */</span></span>
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4391
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<pre style="margin: 0;">-<span id="LC4391" class="line" lang="c"> <span class="idiff left right"> </span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"transcript_diag %d, trstart %d, trend %d, tr_left %u, adj %d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span></span>
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4392
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<pre style="margin: 0;">-<span id="LC4392" class="line" lang="c"> <span class="idiff left right"> </span><span class="n" style="color: #333;">transcript_diag0</span><span class="p">,</span><span class="n" style="color: #333;">trstart</span><span class="p">,</span><span class="n" style="color: #333;">trend</span><span class="p">,</span><span class="n" style="color: #333;">tr_left</span><span class="p">,</span><span class="n" style="color: #333;">adj</span><span class="p">);</span></span>
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4407
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<pre style="margin: 0;">+<span id="LC4407" class="line" lang="c"> <span class="n" style="color: #333;">trend</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">transcript_diag0</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="n" style="color: #333;">querylength</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">querystart</span><span class="p">);</span> <span class="cm" style="color: #998; font-style: italic;">/* tminus */</span></span>
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4408
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<pre style="margin: 0;">+<span id="LC4408" class="line" lang="c"> <span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"transcript_diag %d, trstart %d, trend %d, tr_left %u, adj %d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span></span>
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4409
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<pre style="margin: 0;">+<span id="LC4409" class="line" lang="c"> <span class="n" style="color: #333;">transcript_diag0</span><span class="p">,</span><span class="n" style="color: #333;">trstart</span><span class="p">,</span><span class="n" style="color: #333;">trend</span><span class="p">,</span><span class="n" style="color: #333;">tr_left</span><span class="p">,</span><span class="n" style="color: #333;">adj</span><span class="p">);</span></span>
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4393
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4410
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<pre style="margin: 0;"> <span id="LC4410" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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4394
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<pre style="margin: 0;">-<span id="LC4394" class="line" lang="c"></span>
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4395
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<pre style="margin: 0;">-<span id="LC4395" class="line" lang="c"> <span class="idiff left right"> </span><span class="n" style="color: #333;">exoni</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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4411
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<pre style="margin: 0;">+<span id="LC4411" class="line" lang="c"> </span>
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4412
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<pre style="margin: 0;">+<span id="LC4412" class="line" lang="c"> <span class="n" style="color: #333;">exoni</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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4396
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4413
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<pre style="margin: 0;"> <span id="LC4413" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;">#if 0 && defined(HAVE_AVX2)</span></span>
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4397
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<pre style="margin: 0;">-<span id="LC4397" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> <span class="idiff left right"> </span>_trstart = _mm256_set1_epi32(trstart);</span></span>
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4398
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<pre style="margin: 0;">-<span id="LC4398" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> <span class="idiff left right"> </span>ptr = exonbounds;</span></span>
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4399
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<pre style="margin: 0;">-<span id="LC4399" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> <span class="idiff left right"> </span>_exonbounds = _mm256_loadu_si256((__m256i *) ptr);</span></span>
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4400
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<pre style="margin: 0;">-<span id="LC4400" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> <span class="idiff left right"> </span>_diff = _mm256_cmpgt_epi32(_exonbounds,_trstart);</span></span>
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4401
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<pre style="margin: 0;">-<span id="LC4401" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> <span class="idiff left right"> </span>while (all_zero_p(_diff)) {</span></span>
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4402
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<pre style="margin: 0;">-<span id="LC4402" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> <span class="idiff left right"> </span>exoni += 8;</span></span>
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4403
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<pre style="margin: 0;">-<span id="LC4403" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> <span class="idiff left right"> </span>ptr += 8;</span></span>
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4404
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<pre style="margin: 0;">-<span id="LC4404" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> <span class="idiff left right"> </span>_exonbounds = _mm256_loadu_si256((__m256i *) ptr);</span></span>
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4405
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<pre style="margin: 0;">-<span id="LC4405" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> <span class="idiff left right"> </span>_diff = _mm256_cmpgt_epi32(_exonbounds,_trstart);</span></span>
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4406
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<pre style="margin: 0;">-<span id="LC4406" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> <span class="idiff left right"> </span>}</span></span>
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4407
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<pre style="margin: 0;">-<span id="LC4407" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> <span class="idiff left right"> </span>matchbits = _mm256_movemask_ps(_mm256_castsi256_ps(_diff));</span></span>
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4408
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<pre style="margin: 0;">-<span id="LC4408" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> <span class="idiff left right"> </span>exoni += count_trailing_zeroes_32(matchbits);</span></span>
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4414
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<pre style="margin: 0;">+<span id="LC4414" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> _trstart = _mm256_set1_epi32(trstart);</span></span>
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4415
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<pre style="margin: 0;">+<span id="LC4415" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> ptr = exonbounds;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4416" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4416
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<pre style="margin: 0;">+<span id="LC4416" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> _exonbounds = _mm256_loadu_si256((__m256i *) ptr);</span></span>
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4417
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<pre style="margin: 0;">+<span id="LC4417" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> _diff = _mm256_cmpgt_epi32(_exonbounds,_trstart);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4418" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4418
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<pre style="margin: 0;">+<span id="LC4418" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> while (all_zero_p(_diff)) {</span></span>
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4419
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<pre style="margin: 0;">+<span id="LC4419" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> <span class="idiff left right"> </span>exoni += 8;</span></span>
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4420
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<pre style="margin: 0;">+<span id="LC4420" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> <span class="idiff left right"> </span>ptr += 8;</span></span>
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4421
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<pre style="margin: 0;">+<span id="LC4421" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> <span class="idiff left right"> </span>_exonbounds = _mm256_loadu_si256((__m256i *) ptr);</span></span>
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4422
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<pre style="margin: 0;">+<span id="LC4422" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> <span class="idiff left right"> </span>_diff = _mm256_cmpgt_epi32(_exonbounds,_trstart);</span></span>
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4423
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<pre style="margin: 0;">+<span id="LC4423" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> }</span></span>
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4424
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<pre style="margin: 0;">+<span id="LC4424" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> matchbits = _mm256_movemask_ps(_mm256_castsi256_ps(_diff));</span></span>
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4425
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<pre style="margin: 0;">+<span id="LC4425" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> exoni += count_trailing_zeroes_32(matchbits);</span></span>
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4409
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4426
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<pre style="margin: 0;"> <span id="LC4426" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;">#elif</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">defined</span><span class="p">(</span><span class="n" style="color: #333;">HAVE_SSE2</span><span class="p">)</span></span>
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4410
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<pre style="margin: 0;">-<span id="LC4410" class="line" lang="c"> <span class="idiff left right"> </span><span class="n" style="color: #333;">_trstart</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_set1_epi32</span><span class="p">(</span><span class="n" style="color: #333;">trstart</span><span class="p">);</span></span>
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4411
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<pre style="margin: 0;">-<span id="LC4411" class="line" lang="c"> <span class="idiff left right"> </span><span class="n" style="color: #333;">ptr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">exonbounds</span><span class="p">;</span></span>
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4412
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<pre style="margin: 0;">-<span id="LC4412" class="line" lang="c"> <span class="idiff left right"> </span><span class="n" style="color: #333;">_exonbounds</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_loadu_si128</span><span class="p">((</span><span class="n" style="color: #333;">__m128i</span> <span class="o" style="font-weight: 600;">*</span><span class="p">)</span> <span class="n" style="color: #333;">ptr</span><span class="p">);</span></span>
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4413
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<td class="diff-line-num new_line old" data-linenumber="4427" 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="LC4413" class="line" lang="c"> <span class="idiff left right"> </span><span class="n" style="color: #333;">_diff</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_cmpgt_epi32</span><span class="p">(</span><span class="n" style="color: #333;">_exonbounds</span><span class="p">,</span><span class="n" style="color: #333;">_trstart</span><span class="p">);</span></span>
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4414
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<pre style="margin: 0;">-<span id="LC4414" class="line" lang="c"> <span class="idiff left right"> </span><span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">all_zero_p</span><span class="p">(</span><span class="n" style="color: #333;">_diff</span><span class="p">))</span> <span class="p">{</span></span>
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4415
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<td class="diff-line-num new_line old" data-linenumber="4427" 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="LC4415" class="line" lang="c"> <span class="idiff left right"> </span><span class="n" style="color: #333;">exoni</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">4</span><span class="p">;</span></span>
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4416
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<pre style="margin: 0;">-<span id="LC4416" class="line" lang="c"> <span class="idiff left right"> </span><span class="n" style="color: #333;">ptr</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">4</span><span class="p">;</span></span>
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4417
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<td class="diff-line-num new_line old" data-linenumber="4427" 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="LC4417" class="line" lang="c"> <span class="idiff left right"> </span><span class="n" style="color: #333;">_exonbounds</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_loadu_si128</span><span class="p">((</span><span class="n" style="color: #333;">__m128i</span> <span class="o" style="font-weight: 600;">*</span><span class="p">)</span> <span class="n" style="color: #333;">ptr</span><span class="p">);</span></span>
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4418
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<td class="diff-line-num new_line old" data-linenumber="4427" 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="LC4418" class="line" lang="c"> <span class="idiff left right"> </span><span class="n" style="color: #333;">_diff</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_cmpgt_epi32</span><span class="p">(</span><span class="n" style="color: #333;">_exonbounds</span><span class="p">,</span><span class="n" style="color: #333;">_trstart</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4419" 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">
4419
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<td class="diff-line-num new_line old" data-linenumber="4427" 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="LC4419" class="line" lang="c"> <span class="idiff left right"> </span><span class="p">}</span></span>
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4420
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<td class="diff-line-num new_line old" data-linenumber="4427" 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="LC4420" class="line" lang="c"> <span class="idiff left right"> </span><span class="n" style="color: #333;">matchbits</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_movemask_ps</span><span class="p">(</span><span class="n" style="color: #333;">_mm_castsi128_ps</span><span class="p">(</span><span class="n" style="color: #333;">_diff</span><span class="p">));</span></span>
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4421
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<td class="diff-line-num new_line old" data-linenumber="4427" 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="LC4421" class="line" lang="c"> <span class="idiff left right"> </span><span class="n" style="color: #333;">exoni</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">count_trailing_zeroes_32</span><span class="p">(</span><span class="n" style="color: #333;">matchbits</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4427" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4427
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<pre style="margin: 0;">+<span id="LC4427" class="line" lang="c"> <span class="n" style="color: #333;">_trstart</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_set1_epi32</span><span class="p">(</span><span class="n" style="color: #333;">trstart</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4428" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4428
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<pre style="margin: 0;">+<span id="LC4428" class="line" lang="c"> <span class="n" style="color: #333;">ptr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">exonbounds</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4429" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4429
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<pre style="margin: 0;">+<span id="LC4429" class="line" lang="c"> <span class="n" style="color: #333;">_exonbounds</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_loadu_si128</span><span class="p">((</span><span class="n" style="color: #333;">__m128i</span> <span class="o" style="font-weight: 600;">*</span><span class="p">)</span> <span class="n" style="color: #333;">ptr</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4430" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4430
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<pre style="margin: 0;">+<span id="LC4430" class="line" lang="c"> <span class="n" style="color: #333;">_diff</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_cmpgt_epi32</span><span class="p">(</span><span class="n" style="color: #333;">_exonbounds</span><span class="p">,</span><span class="n" style="color: #333;">_trstart</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4431" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4431
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<pre style="margin: 0;">+<span id="LC4431" class="line" lang="c"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">all_zero_p</span><span class="p">(</span><span class="n" style="color: #333;">_diff</span><span class="p">))</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4432" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4432
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<pre style="margin: 0;">+<span id="LC4432" class="line" lang="c"> <span class="idiff left right"> </span><span class="n" style="color: #333;">exoni</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">4</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4433" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4433
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<pre style="margin: 0;">+<span id="LC4433" class="line" lang="c"> <span class="idiff left right"> </span><span class="n" style="color: #333;">ptr</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">4</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4434" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4434
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<pre style="margin: 0;">+<span id="LC4434" class="line" lang="c"> <span class="idiff left right"> </span><span class="n" style="color: #333;">_exonbounds</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_loadu_si128</span><span class="p">((</span><span class="n" style="color: #333;">__m128i</span> <span class="o" style="font-weight: 600;">*</span><span class="p">)</span> <span class="n" style="color: #333;">ptr</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4435" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4435
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<pre style="margin: 0;">+<span id="LC4435" class="line" lang="c"> <span class="idiff left right"> </span><span class="n" style="color: #333;">_diff</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_cmpgt_epi32</span><span class="p">(</span><span class="n" style="color: #333;">_exonbounds</span><span class="p">,</span><span class="n" style="color: #333;">_trstart</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4436" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4436
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<pre style="margin: 0;">+<span id="LC4436" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4437" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4437
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<pre style="margin: 0;">+<span id="LC4437" class="line" lang="c"> <span class="n" style="color: #333;">matchbits</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_mm_movemask_ps</span><span class="p">(</span><span class="n" style="color: #333;">_mm_castsi128_ps</span><span class="p">(</span><span class="n" style="color: #333;">_diff</span><span class="p">));</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4438" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4438
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<pre style="margin: 0;">+<span id="LC4438" class="line" lang="c"> <span class="n" style="color: #333;">exoni</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">count_trailing_zeroes_32</span><span class="p">(</span><span class="n" style="color: #333;">matchbits</span><span class="p">);</span></span>
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4422
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4439
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<pre style="margin: 0;"> <span id="LC4439" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#else</span></span>
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4423
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<pre style="margin: 0;">-<span id="LC4423" class="line" lang="c"> <span class="idiff left right"> </span><span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">exoni</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">nexons</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">exonbounds</span><span class="p">[</span><span class="n" style="color: #333;">exoni</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">trstart</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4424" 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">
4424
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<td class="diff-line-num new_line old" data-linenumber="4440" 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="LC4424" class="line" lang="c"> <span class="idiff left right"> </span><span class="n" style="color: #333;">exoni</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4425" 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">
4425
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<td class="diff-line-num new_line old" data-linenumber="4440" 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="LC4425" class="line" lang="c"> <span class="idiff left right"> </span><span class="p">}</span></span>
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<td class="diff-line-num new old_line" data-linenumber="4426" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="4440" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4440
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<pre style="margin: 0;">+<span id="LC4440" class="line" lang="c"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">exoni</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">nexons</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">exonbounds</span><span class="p">[</span><span class="n" style="color: #333;">exoni</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">trstart</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4441" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4441
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<pre style="margin: 0;">+<span id="LC4441" class="line" lang="c"> <span class="idiff left right"> </span><span class="n" style="color: #333;">exoni</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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<td class="diff-line-num new old_line" data-linenumber="4426" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="4442" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4442
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<pre style="margin: 0;">+<span id="LC4442" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="4426" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4426
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<td class="diff-line-num new_line" data-linenumber="4443" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4443
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<pre style="margin: 0;"> <span id="LC4443" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4427" 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">
4427
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<td class="diff-line-num new_line old" data-linenumber="4444" 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="LC4427" class="line" lang="c"></span>
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<td class="diff-line-num old old_line" data-linenumber="4428" 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">
4428
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<td class="diff-line-num new_line old" data-linenumber="4444" 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="LC4428" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">exoni</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">nexons</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4429" 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">
4429
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<td class="diff-line-num new_line old" data-linenumber="4444" 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="LC4429" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"ABORTING BECAUSE OF EXONI %d >= NEXONS %d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">exoni</span><span class="p">,</span><span class="n" style="color: #333;">nexons</span><span class="p">));</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4430" 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">
4430
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<td class="diff-line-num new_line old" data-linenumber="4444" 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="LC4430" class="line" lang="c"> <span class="n" style="color: #333;">abortp</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4431" 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">
4431
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<td class="diff-line-num new_line old" data-linenumber="4444" 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="LC4431" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4432" 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">
4432
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<td class="diff-line-num new_line old" data-linenumber="4444" 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="LC4432" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"(15) exoni %d out of nexons %d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">exoni</span><span class="p">,</span><span class="n" style="color: #333;">nexons</span><span class="p">));</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4433" 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">
4433
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<td class="diff-line-num new_line old" data-linenumber="4444" 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="LC4433" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">exoni</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4434" 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">
4434
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<td class="diff-line-num new_line old" data-linenumber="4444" 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="LC4434" class="line" lang="c"> <span class="n" style="color: #333;">exonpos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">trstart</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4435" 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">
4435
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<td class="diff-line-num new_line old" data-linenumber="4444" 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="LC4435" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4436" 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">
4436
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<td class="diff-line-num new_line old" data-linenumber="4444" 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="LC4436" class="line" lang="c"> <span class="n" style="color: #333;">exonpos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">trstart</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">exonbounds</span><span class="p">[</span><span class="n" style="color: #333;">exoni</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 old old_line" data-linenumber="4437" 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">
4437
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<td class="diff-line-num new_line old" data-linenumber="4444" 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="LC4437" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4438" 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">
4438
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<td class="diff-line-num new_line old" data-linenumber="4444" 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="LC4438" class="line" lang="c"> <span class="n" style="color: #333;">exon_residual</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">exonbounds</span><span class="p">[</span><span class="n" style="color: #333;">exoni</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">trstart</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4439" 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">
4439
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<td class="diff-line-num new_line old" data-linenumber="4444" 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="LC4439" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"exoni %d => exon_residual %d, exonpos %d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">exoni</span><span class="p">,</span><span class="n" style="color: #333;">exon_residual</span><span class="p">,</span><span class="n" style="color: #333;">exonpos</span><span class="p">));</span></span>
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4440
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<td class="diff-line-num new_line old" data-linenumber="4444" 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="LC4440" class="line" lang="c"></span>
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4441
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<pre style="margin: 0;">-<span id="LC4441" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Generate one substring per exon */</span></span>
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4442
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<pre style="margin: 0;">-<span id="LC4442" class="line" lang="c"> <span class="n" style="color: #333;">genomicpos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">exonstarts</span><span class="p">[</span><span class="n" style="color: #333;">exoni</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">exonpos</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/* gminus */</span></span>
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4443
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<pre style="margin: 0;">-<span id="LC4443" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"genomicpos %u = %u - %u</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">genomicpos</span><span class="p">,</span><span class="n" style="color: #333;">exonstarts</span><span class="p">[</span><span class="n" style="color: #333;">exoni</span><span class="p">],</span><span class="n" style="color: #333;">exonpos</span><span class="p">));</span></span>
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4444
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<pre style="margin: 0;">-<span id="LC4444" class="line" lang="c"> <span class="n" style="color: #333;">align_residual</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">queryend</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">querystart</span><span class="p">;</span></span>
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4445
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<pre style="margin: 0;">-<span id="LC4445" class="line" lang="c"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">align_residual</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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4446
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<pre style="margin: 0;">-<span id="LC4446" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"abortp %d, align_residual %d, exon_residual %d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">abortp</span><span class="p">,</span><span class="n" style="color: #333;">align_residual</span><span class="p">,</span><span class="n" style="color: #333;">exon_residual</span><span class="p">));</span></span>
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4447
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<td class="diff-line-num new_line old" data-linenumber="4444" 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="LC4447" class="line" lang="c"> <span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">align_residual</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">exon_residual</span><span class="p">)</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">align_residual</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">exon_residual</span><span class="p">;</span></span>
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4448
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<td class="diff-line-num new_line old" data-linenumber="4444" 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="LC4448" class="line" lang="c"> <span class="n" style="color: #333;">querystart</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">queryend</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">len</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/* tminus */</span></span>
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4449
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<pre style="margin: 0;">-<span id="LC4449" class="line" lang="c"> </span>
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4450
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<pre style="margin: 0;">-<span id="LC4450" class="line" lang="c"> <span class="n" style="color: #333;">alignend</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">chroffset</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">genomicpos</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4451" 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">
4451
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<td class="diff-line-num new_line old" data-linenumber="4444" 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="LC4451" class="line" lang="c"> <span class="n" style="color: #333;">alignstart</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alignend</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">len</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/* gminus */</span></span>
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4452
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<td class="diff-line-num new_line old" data-linenumber="4444" 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="LC4452" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">left</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alignstart</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">querystart</span><span class="p">);</span> <span class="cm" style="color: #998; font-style: italic;">/* tminus == gminus */</span></span>
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4453
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<td class="diff-line-num new_line old" data-linenumber="4444" 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="LC4453" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"tr ultrafast gap case 4 1st part query %d..%d, align %u..%u [%u..%u], left %u = %u - %d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4454" 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">
4454
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<td class="diff-line-num new_line old" data-linenumber="4444" 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="LC4454" class="line" lang="c"> <span class="n" style="color: #333;">querystart</span><span class="p">,</span><span class="n" style="color: #333;">queryend</span><span class="p">,</span><span class="n" style="color: #333;">alignstart</span><span class="p">,</span><span class="n" style="color: #333;">alignend</span><span class="p">,</span><span class="n" style="color: #333;">alignstart</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">chroffset</span><span class="p">,</span><span class="n" style="color: #333;">alignend</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">chroffset</span><span class="p">,</span></span>
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4455
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<pre style="margin: 0;">-<span id="LC4455" class="line" lang="c"> <span class="n" style="color: #333;">left</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">chroffset</span><span class="p">,</span><span class="n" style="color: #333;">alignstart</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">chroffset</span><span class="p">,</span><span class="n" style="color: #333;">querystart</span><span class="p">));</span></span>
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4456
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<pre style="margin: 0;">-<span id="LC4456" class="line" lang="c"></span>
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4457
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<pre style="margin: 0;">-<span id="LC4457" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* tminus: push alignend first */</span></span>
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4458
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<pre style="margin: 0;">-<span id="LC4458" class="line" lang="c"> <span class="n" style="color: #333;">endpoints</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Uintlist_push</span><span class="p">(</span><span class="n" style="color: #333;">endpoints</span><span class="p">,(</span><span class="n" style="color: #333;">Chrpos_T</span><span class="p">)</span> <span class="p">(</span><span class="n" style="color: #333;">alignend</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">chroffset</span><span class="p">));</span></span>
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4459
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<pre style="margin: 0;">-<span id="LC4459" class="line" lang="c"> <span class="n" style="color: #333;">endpoints</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Uintlist_push</span><span class="p">(</span><span class="n" style="color: #333;">endpoints</span><span class="p">,(</span><span class="n" style="color: #333;">Chrpos_T</span><span class="p">)</span> <span class="p">(</span><span class="n" style="color: #333;">alignstart</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">chroffset</span><span class="p">));</span></span>
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4460
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<pre style="margin: 0;">-<span id="LC4460" class="line" lang="c"></span>
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4461
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<td class="diff-line-num new_line old" data-linenumber="4444" 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="LC4461" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">align_residual</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">exon_residual</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4462" 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">
4462
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<td class="diff-line-num new_line old" data-linenumber="4444" 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="LC4462" class="line" lang="c"> <span class="n" style="color: #333;">exon_residual</span> <span class="o" style="font-weight: 600;">-=</span> <span class="n" style="color: #333;">align_residual</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/* Need to know this if we have a following deletion */</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4463" 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">
4463
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<td class="diff-line-num new_line old" data-linenumber="4444" 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="LC4463" class="line" lang="c"> <span class="n" style="color: #333;">align_residual</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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4464
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<td class="diff-line-num new_line old" data-linenumber="4444" 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="LC4464" class="line" lang="c"> <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="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">exoni</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">nexons</span><span class="p">)</span> <span class="p">{</span></span>
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4465
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<td class="diff-line-num new_line old" data-linenumber="4444" 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="LC4465" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Aligning past the end of the transcript */</span></span>
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4466
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<td class="diff-line-num new_line old" data-linenumber="4444" 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="LC4466" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"8 ABORTING BECAUSE ALIGNING PAST END OF TRANSCRIPT</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">));</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4467" 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">
4467
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<td class="diff-line-num new_line old" data-linenumber="4444" 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="LC4467" class="line" lang="c"> <span class="n" style="color: #333;">align_residual</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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4468
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<td class="diff-line-num new_line old" data-linenumber="4444" 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="LC4468" class="line" lang="c"> <span class="n" style="color: #333;">abortp</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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4469
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<td class="diff-line-num new_line old" data-linenumber="4444" 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="LC4469" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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4470
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<td class="diff-line-num new_line old" data-linenumber="4444" 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="LC4470" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* nintrons += 1; */</span></span>
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4471
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<td class="diff-line-num new_line old" data-linenumber="4444" 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="LC4471" class="line" lang="c"> <span class="n" style="color: #333;">align_residual</span> <span class="o" style="font-weight: 600;">-=</span> <span class="n" style="color: #333;">len</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4472" 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">
4472
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<td class="diff-line-num new_line old" data-linenumber="4444" 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="LC4472" class="line" lang="c"> <span class="n" style="color: #333;">queryend</span> <span class="o" style="font-weight: 600;">-=</span> <span class="n" style="color: #333;">len</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/* tminus */</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4473" 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">
4473
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<td class="diff-line-num new_line old" data-linenumber="4444" 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="LC4473" class="line" lang="c"> <span class="n" style="color: #333;">genomicpos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">exonstarts</span><span class="p">[</span><span class="n" style="color: #333;">exoni</span><span class="p">];</span> <span class="cm" style="color: #998; font-style: italic;">/* gminus */</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4474" 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">
4474
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<td class="diff-line-num new_line old" data-linenumber="4444" 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="LC4474" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"genomicpos %u = %u</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">genomicpos</span><span class="p">,</span><span class="n" style="color: #333;">exonstarts</span><span class="p">[</span><span class="n" style="color: #333;">exoni</span><span class="p">]));</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4475" 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">
4475
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<td class="diff-line-num new_line old" data-linenumber="4444" 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="LC4475" class="line" lang="c"> <span class="n" style="color: #333;">exon_residual</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">exonbounds</span><span class="p">[</span><span class="n" style="color: #333;">exoni</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">exonbounds</span><span class="p">[</span><span class="n" style="color: #333;">exoni</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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4476
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<td class="diff-line-num new_line old" data-linenumber="4444" 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="LC4476" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"INTRON</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">));</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4477" 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">
4477
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<td class="diff-line-num new_line old" data-linenumber="4444" 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="LC4477" class="line" lang="c"> <span class="n" style="color: #333;">gaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Intlist_push</span><span class="p">(</span><span class="n" style="color: #333;">gaps</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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4478
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<td class="diff-line-num new_line old" data-linenumber="4444" 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="LC4478" class="line" lang="c"> <span class="p">}</span></span>
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4479
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<td class="diff-line-num new_line old" data-linenumber="4444" 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="LC4479" class="line" lang="c"> <span class="p">}</span></span>
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4480
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<pre style="margin: 0;">-<span id="LC4480" class="line" lang="c"> <span class="p">}</span></span>
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4481
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<td class="diff-line-num new_line old" data-linenumber="4444" 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="LC4481" class="line" lang="c"></span>
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<td class="diff-line-num old old_line" data-linenumber="4482" 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">
4482
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<td class="diff-line-num new_line old" data-linenumber="4444" 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="LC4482" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* gap */</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4483" 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">
4483
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<td class="diff-line-num new_line old" data-linenumber="4444" 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="LC4483" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"INDEL: last piece %d | nindels %d | next piece %d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">len</span><span class="p">,</span><span class="n" style="color: #333;">nindels</span><span class="p">,</span><span class="n" style="color: #333;">exon_residual</span><span class="p">));</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4484" 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">
4484
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<td class="diff-line-num new_line old" data-linenumber="4444" 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="LC4484" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"exon residual %d vs nindels %d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">exon_residual</span><span class="p">,</span><span class="n" style="color: #333;">nindels</span><span class="p">));</span></span>
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4485
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<td class="diff-line-num new_line old" data-linenumber="4444" 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="LC4485" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">abortp</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4486" 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">
4486
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<td class="diff-line-num new_line old" data-linenumber="4444" 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="LC4486" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Skip */</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4487" 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">
4487
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<td class="diff-line-num new_line old" data-linenumber="4444" 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="LC4487" class="line" lang="c"> <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="cm" style="color: #998; font-style: italic;">/*len <= nindels ||*/</span><span class="n" style="color: #333;">exon_residual</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">nindels</span><span class="p">)</span> <span class="p">{</span></span>
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4488
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<td class="diff-line-num new_line old" data-linenumber="4444" 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="LC4488" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"ABORTING BECAUSE INDEL OVERLAPS SPLICE SITE</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">));</span></span>
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<td class="diff-line-num new old_line" data-linenumber="4489" style="width: 35px; color: rgba(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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4444
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<pre style="margin: 0;">+<span id="LC4444" class="line" lang="c"> </span>
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<td class="diff-line-num new new_line" data-linenumber="4445" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4445
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<pre style="margin: 0;">+<span id="LC4445" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">exoni</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">nexons</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4446" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4446
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<pre style="margin: 0;">+<span id="LC4446" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"ABORTING BECAUSE OF EXONI %d >= NEXONS %d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">exoni</span><span class="p">,</span><span class="n" style="color: #333;">nexons</span><span class="p">));</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4447" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4447
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<pre style="margin: 0;">+<span id="LC4447" class="line" lang="c"> <span class="n" style="color: #333;">abortp</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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<td class="diff-line-num new old_line" data-linenumber="4489" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="4448" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4448
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<pre style="margin: 0;">+<span id="LC4448" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="diff-line-num new old_line" data-linenumber="4489" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="4449" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4449
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<pre style="margin: 0;">+<span id="LC4449" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"(15) exoni %d out of nexons %d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">exoni</span><span class="p">,</span><span class="n" style="color: #333;">nexons</span><span class="p">));</span></span>
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<td class="diff-line-num new old_line" data-linenumber="4489" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="4450" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4450
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<pre style="margin: 0;">+<span id="LC4450" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">exoni</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new old_line" data-linenumber="4489" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="4451" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4451
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<pre style="margin: 0;">+<span id="LC4451" class="line" lang="c"> <span class="n" style="color: #333;">exonpos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">trstart</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4452" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4452
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<pre style="margin: 0;">+<span id="LC4452" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="diff-line-num new old_line" data-linenumber="4489" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="4453" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4453
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<pre style="margin: 0;">+<span id="LC4453" class="line" lang="c"> <span class="n" style="color: #333;">exonpos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">trstart</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">exonbounds</span><span class="p">[</span><span class="n" style="color: #333;">exoni</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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4454
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<pre style="margin: 0;">+<span id="LC4454" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4455" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4455
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<pre style="margin: 0;">+<span id="LC4455" class="line" lang="c"> <span class="n" style="color: #333;">exon_residual</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">exonbounds</span><span class="p">[</span><span class="n" style="color: #333;">exoni</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">trstart</span><span class="p">;</span></span>
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4456
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<pre style="margin: 0;">+<span id="LC4456" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"exoni %d => exon_residual %d, exonpos %d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">exoni</span><span class="p">,</span><span class="n" style="color: #333;">exon_residual</span><span class="p">,</span><span class="n" style="color: #333;">exonpos</span><span class="p">));</span></span>
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4457
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<pre style="margin: 0;">+<span id="LC4457" class="line" lang="c"> </span>
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<td class="diff-line-num new new_line" data-linenumber="4458" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4458
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<pre style="margin: 0;">+<span id="LC4458" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Generate one substring per exon */</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4459" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4459
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<pre style="margin: 0;">+<span id="LC4459" class="line" lang="c"> <span class="n" style="color: #333;">genomicpos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">exonstarts</span><span class="p">[</span><span class="n" style="color: #333;">exoni</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">exonpos</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/* gminus */</span></span>
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4460
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<pre style="margin: 0;">+<span id="LC4460" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"genomicpos %u = %u - %u</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">genomicpos</span><span class="p">,</span><span class="n" style="color: #333;">exonstarts</span><span class="p">[</span><span class="n" style="color: #333;">exoni</span><span class="p">],</span><span class="n" style="color: #333;">exonpos</span><span class="p">));</span></span>
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4461
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<pre style="margin: 0;">+<span id="LC4461" class="line" lang="c"> <span class="n" style="color: #333;">align_residual</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">queryend</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">querystart</span><span class="p">;</span></span>
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4462
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<pre style="margin: 0;">+<span id="LC4462" class="line" lang="c"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">align_residual</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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4463
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<pre style="margin: 0;">+<span id="LC4463" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"abortp %d, align_residual %d, exon_residual %d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">abortp</span><span class="p">,</span><span class="n" style="color: #333;">align_residual</span><span class="p">,</span><span class="n" style="color: #333;">exon_residual</span><span class="p">));</span></span>
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4464
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<pre style="margin: 0;">+<span id="LC4464" class="line" lang="c"> <span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">align_residual</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">exon_residual</span><span class="p">)</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">align_residual</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">exon_residual</span><span class="p">;</span></span>
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4465
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<pre style="margin: 0;">+<span id="LC4465" class="line" lang="c"> <span class="n" style="color: #333;">querystart</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">queryend</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">len</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/* tminus */</span></span>
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4466
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<pre style="margin: 0;">+<span id="LC4466" class="line" lang="c"> </span>
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4467
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<pre style="margin: 0;">+<span id="LC4467" class="line" lang="c"> <span class="n" style="color: #333;">alignend</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">chroffset</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">genomicpos</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4468" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4468
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<pre style="margin: 0;">+<span id="LC4468" class="line" lang="c"> <span class="n" style="color: #333;">alignstart</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alignend</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">len</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/* gminus */</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4469" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4469
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<pre style="margin: 0;">+<span id="LC4469" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">left</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alignstart</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">querystart</span><span class="p">);</span> <span class="cm" style="color: #998; font-style: italic;">/* tminus == gminus */</span></span>
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4470
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<pre style="margin: 0;">+<span id="LC4470" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"tr ultrafast gap case 4 1st part query %d..%d, align %u..%u [%u..%u], left %u = %u - %d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span></span>
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4471
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<pre style="margin: 0;">+<span id="LC4471" class="line" lang="c"> <span class="n" style="color: #333;">querystart</span><span class="p">,</span><span class="n" style="color: #333;">queryend</span><span class="p">,</span><span class="n" style="color: #333;">alignstart</span><span class="p">,</span><span class="n" style="color: #333;">alignend</span><span class="p">,</span><span class="n" style="color: #333;">alignstart</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">chroffset</span><span class="p">,</span><span class="n" style="color: #333;">alignend</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">chroffset</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4472" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4472
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<pre style="margin: 0;">+<span id="LC4472" class="line" lang="c"> <span class="n" style="color: #333;">left</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">chroffset</span><span class="p">,</span><span class="n" style="color: #333;">alignstart</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">chroffset</span><span class="p">,</span><span class="n" style="color: #333;">querystart</span><span class="p">));</span></span>
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4473
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<pre style="margin: 0;">+<span id="LC4473" class="line" lang="c"> </span>
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4474
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<pre style="margin: 0;">+<span id="LC4474" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* tminus: push alignend first */</span></span>
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4475
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<pre style="margin: 0;">+<span id="LC4475" class="line" lang="c"> <span class="n" style="color: #333;">endpoints</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Uintlist_push</span><span class="p">(</span><span class="n" style="color: #333;">endpoints</span><span class="p">,(</span><span class="n" style="color: #333;">Chrpos_T</span><span class="p">)</span> <span class="p">(</span><span class="n" style="color: #333;">alignend</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">chroffset</span><span class="p">));</span></span>
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4476
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<pre style="margin: 0;">+<span id="LC4476" class="line" lang="c"> <span class="n" style="color: #333;">endpoints</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Uintlist_push</span><span class="p">(</span><span class="n" style="color: #333;">endpoints</span><span class="p">,(</span><span class="n" style="color: #333;">Chrpos_T</span><span class="p">)</span> <span class="p">(</span><span class="n" style="color: #333;">alignstart</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">chroffset</span><span class="p">));</span></span>
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4477
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<pre style="margin: 0;">+<span id="LC4477" class="line" lang="c"> </span>
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4478
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<pre style="margin: 0;">+<span id="LC4478" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">align_residual</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">exon_residual</span><span class="p">)</span> <span class="p">{</span></span>
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4479
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<pre style="margin: 0;">+<span id="LC4479" class="line" lang="c"> <span class="n" style="color: #333;">exon_residual</span> <span class="o" style="font-weight: 600;">-=</span> <span class="n" style="color: #333;">align_residual</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/* Need to know this if we have a following deletion */</span></span>
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4480
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<pre style="margin: 0;">+<span id="LC4480" class="line" lang="c"> <span class="n" style="color: #333;">align_residual</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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4481
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<pre style="margin: 0;">+<span id="LC4481" class="line" lang="c"> <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="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">exoni</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">nexons</span><span class="p">)</span> <span class="p">{</span></span>
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4482
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<pre style="margin: 0;">+<span id="LC4482" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Aligning past the end of the transcript */</span></span>
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4483
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<pre style="margin: 0;">+<span id="LC4483" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"8 ABORTING BECAUSE ALIGNING PAST END OF TRANSCRIPT</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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4484
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<pre style="margin: 0;">+<span id="LC4484" class="line" lang="c"> <span class="n" style="color: #333;">align_residual</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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4489
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4485
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<pre style="margin: 0;"> <span id="LC4485" class="line" lang="c"> <span class="n" style="color: #333;">abortp</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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4490
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4486
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<pre style="margin: 0;"> <span id="LC4486" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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4491
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<pre style="margin: 0;">-<span id="LC4491" class="line" lang="c"> <span class="n" style="color: #333;">gaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Intlist_push</span><span class="p">(</span><span class="n" style="color: #333;">gaps</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;">adj</span><span class="p">);</span></span>
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4492
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<pre style="margin: 0;">-<span id="LC4492" class="line" lang="c"> <span class="p">}</span></span>
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4493
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<pre style="margin: 0;">-<span id="LC4493" class="line" lang="c"></span>
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4494
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<pre style="margin: 0;">-<span id="LC4494" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* second part */</span></span>
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4495
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<pre style="margin: 0;">-<span id="LC4495" class="line" lang="c"> <span class="n" style="color: #333;">tr_left</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tr_left1</span><span class="p">;</span></span>
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4496
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<pre style="margin: 0;">-<span id="LC4496" class="line" lang="c"> <span class="n" style="color: #333;">queryend</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">querylength</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">indel_pos</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">ninserts</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/* tminus: compute from queryend to querystart */</span></span>
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4497
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<pre style="margin: 0;">-<span id="LC4497" class="line" lang="c"> <span class="n" style="color: #333;">querystart</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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4498
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<pre style="margin: 0;">-<span id="LC4498" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</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;">Analyzing query %d..%d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">querystart</span><span class="p">,</span><span class="n" style="color: #333;">queryend</span><span class="p">));</span></span>
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4499
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<td class="diff-line-num new_line old" data-linenumber="4487" 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="LC4499" class="line" lang="c"></span>
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4500
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<td class="diff-line-num new_line old" data-linenumber="4487" 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="LC4500" class="line" lang="c"> <span class="n" style="color: #333;">trstart</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">transcript_diag1</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="n" style="color: #333;">querylength</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">queryend</span><span class="p">);</span> <span class="cm" style="color: #998; font-style: italic;">/* tminus */</span></span>
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4501
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<td class="diff-line-num new_line old" data-linenumber="4487" 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="LC4501" class="line" lang="c"> <span class="n" style="color: #333;">overall_trend</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">transcript_diag1</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="n" style="color: #333;">querylength</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">querystart</span><span class="p">);</span> <span class="cm" style="color: #998; font-style: italic;">/* tminus */</span></span>
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4502
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<td class="diff-line-num new_line old" data-linenumber="4487" 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="LC4502" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"transcript_diag %d, trstart %d, trend %d, tr_left %u</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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4503
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<td class="diff-line-num new_line old" data-linenumber="4487" 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="LC4503" class="line" lang="c"> <span class="n" style="color: #333;">transcript_diag1</span><span class="p">,</span><span class="n" style="color: #333;">trstart</span><span class="p">,</span><span class="n" style="color: #333;">overall_trend</span><span class="p">,</span><span class="n" style="color: #333;">tr_left</span><span class="p">));</span></span>
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4504
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<td class="diff-line-num new_line old" data-linenumber="4487" 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="LC4504" class="line" lang="c"></span>
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4505
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<td class="diff-line-num new_line old" data-linenumber="4487" 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="LC4505" class="line" lang="c"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">exoni</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">nexons</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">exonbounds</span><span class="p">[</span><span class="n" style="color: #333;">exoni</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">trstart</span><span class="p">)</span> <span class="p">{</span></span>
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4506
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<td class="diff-line-num new_line old" data-linenumber="4487" 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="LC4506" class="line" lang="c"> <span class="n" style="color: #333;">exoni</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4487" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4487
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<pre style="margin: 0;">+<span id="LC4487" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* nintrons += 1; */</span></span>
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4488
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<pre style="margin: 0;">+<span id="LC4488" class="line" lang="c"> <span class="n" style="color: #333;">align_residual</span> <span class="o" style="font-weight: 600;">-=</span> <span class="n" style="color: #333;">len</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4489" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4489
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<pre style="margin: 0;">+<span id="LC4489" class="line" lang="c"> <span class="n" style="color: #333;">queryend</span> <span class="o" style="font-weight: 600;">-=</span> <span class="n" style="color: #333;">len</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/* tminus */</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4490" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4490
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<pre style="margin: 0;">+<span id="LC4490" class="line" lang="c"> <span class="n" style="color: #333;">genomicpos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">exonstarts</span><span class="p">[</span><span class="n" style="color: #333;">exoni</span><span class="p">];</span> <span class="cm" style="color: #998; font-style: italic;">/* gminus */</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4491" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4491
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<pre style="margin: 0;">+<span id="LC4491" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"genomicpos %u = %u</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">genomicpos</span><span class="p">,</span><span class="n" style="color: #333;">exonstarts</span><span class="p">[</span><span class="n" style="color: #333;">exoni</span><span class="p">]));</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4492" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4492
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<pre style="margin: 0;">+<span id="LC4492" class="line" lang="c"> <span class="n" style="color: #333;">exon_residual</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">exonbounds</span><span class="p">[</span><span class="n" style="color: #333;">exoni</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">exonbounds</span><span class="p">[</span><span class="n" style="color: #333;">exoni</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">];</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4493" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4493
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<pre style="margin: 0;">+<span id="LC4493" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"INTRON</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">));</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4494" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4494
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<pre style="margin: 0;">+<span id="LC4494" class="line" lang="c"> <span class="n" style="color: #333;">gaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Intlist_push</span><span class="p">(</span><span class="n" style="color: #333;">gaps</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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4507
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4495
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<pre style="margin: 0;"> <span id="LC4495" class="line" lang="c"> <span class="p">}</span></span>
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4508
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<td class="diff-line-num new_line old" data-linenumber="4496" 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="LC4508" class="line" lang="c"></span>
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4509
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<td class="diff-line-num new_line old" data-linenumber="4496" 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="LC4509" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">exoni</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">nexons</span><span class="p">)</span> <span class="p">{</span></span>
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4510
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<pre style="margin: 0;">-<span id="LC4510" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"ABORTING BECAUSE OF EXONI %d >= NEXONS %d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">exoni</span><span class="p">,</span><span class="n" style="color: #333;">nexons</span><span class="p">));</span></span>
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4496
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<pre style="margin: 0;">+<span id="LC4496" class="line" lang="c"> <span class="p">}</span></span>
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4497
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<pre style="margin: 0;">+<span id="LC4497" class="line" lang="c"> <span class="p">}</span></span>
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4498
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<pre style="margin: 0;">+<span id="LC4498" class="line" lang="c"> </span>
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4499
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<pre style="margin: 0;">+<span id="LC4499" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* gap */</span></span>
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4500
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<pre style="margin: 0;">+<span id="LC4500" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"INDEL: last piece %d | nindels %d | next piece %d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">len</span><span class="p">,</span><span class="n" style="color: #333;">nindels</span><span class="p">,</span><span class="n" style="color: #333;">exon_residual</span><span class="p">));</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4501" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4501
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<pre style="margin: 0;">+<span id="LC4501" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"exon residual %d vs nindels %d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">exon_residual</span><span class="p">,</span><span class="n" style="color: #333;">nindels</span><span class="p">));</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4502" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4502
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<pre style="margin: 0;">+<span id="LC4502" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">abortp</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4503" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4503
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<pre style="margin: 0;">+<span id="LC4503" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Skip */</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4504" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4504
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<pre style="margin: 0;">+<span id="LC4504" class="line" lang="c"> <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="cm" style="color: #998; font-style: italic;">/*len <= nindels ||*/</span><span class="n" style="color: #333;">exon_residual</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">nindels</span><span class="p">)</span> <span class="p">{</span></span>
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4505
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<pre style="margin: 0;">+<span id="LC4505" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"ABORTING BECAUSE INDEL OVERLAPS SPLICE SITE (8)</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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4506
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<pre style="margin: 0;">+<span id="LC4506" class="line" lang="c"> <span class="n" style="color: #333;">abortp</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4507" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4507
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<pre style="margin: 0;">+<span id="LC4507" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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4508
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<pre style="margin: 0;">+<span id="LC4508" class="line" lang="c"> <span class="n" style="color: #333;">gaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Intlist_push</span><span class="p">(</span><span class="n" style="color: #333;">gaps</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;">adj</span><span class="p">);</span></span>
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4509
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<pre style="margin: 0;">+<span id="LC4509" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4510" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4510
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<pre style="margin: 0;">+<span id="LC4510" class="line" lang="c"> </span>
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4511
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<pre style="margin: 0;">+<span id="LC4511" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* second part */</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4512" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4512
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<pre style="margin: 0;">+<span id="LC4512" class="line" lang="c"> <span class="n" style="color: #333;">tr_left</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tr_left1</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4513" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4513
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<pre style="margin: 0;">+<span id="LC4513" class="line" lang="c"> <span class="n" style="color: #333;">queryend</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">querylength</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">indel_pos</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">ninserts</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/* tminus: compute from queryend to querystart */</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4514" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4514
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<pre style="margin: 0;">+<span id="LC4514" class="line" lang="c"> <span class="n" style="color: #333;">querystart</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4515" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4515
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<pre style="margin: 0;">+<span id="LC4515" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</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;">Analyzing query %d..%d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">querystart</span><span class="p">,</span><span class="n" style="color: #333;">queryend</span><span class="p">));</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4516" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4516
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<pre style="margin: 0;">+<span id="LC4516" class="line" lang="c"> </span>
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<td class="diff-line-num new new_line" data-linenumber="4517" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4517
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<pre style="margin: 0;">+<span id="LC4517" class="line" lang="c"> <span class="n" style="color: #333;">trstart</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">transcript_diag1</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="n" style="color: #333;">querylength</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">queryend</span><span class="p">);</span> <span class="cm" style="color: #998; font-style: italic;">/* tminus */</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4518" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4518
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<pre style="margin: 0;">+<span id="LC4518" class="line" lang="c"> <span class="n" style="color: #333;">overall_trend</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">transcript_diag1</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="n" style="color: #333;">querylength</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">querystart</span><span class="p">);</span> <span class="cm" style="color: #998; font-style: italic;">/* tminus */</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4519" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4519
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<pre style="margin: 0;">+<span id="LC4519" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"transcript_diag %d, trstart %d, trend %d, tr_left %u</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4520" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4520
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<pre style="margin: 0;">+<span id="LC4520" class="line" lang="c"> <span class="n" style="color: #333;">transcript_diag1</span><span class="p">,</span><span class="n" style="color: #333;">trstart</span><span class="p">,</span><span class="n" style="color: #333;">overall_trend</span><span class="p">,</span><span class="n" style="color: #333;">tr_left</span><span class="p">));</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4521" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4521
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<pre style="margin: 0;">+<span id="LC4521" class="line" lang="c"> </span>
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<td class="diff-line-num new new_line" data-linenumber="4522" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4522
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<pre style="margin: 0;">+<span id="LC4522" class="line" lang="c"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">exoni</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">nexons</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">exonbounds</span><span class="p">[</span><span class="n" style="color: #333;">exoni</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">trstart</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4523" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4523
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<pre style="margin: 0;">+<span id="LC4523" class="line" lang="c"> <span class="n" style="color: #333;">exoni</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4524" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4524
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<pre style="margin: 0;">+<span id="LC4524" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4525" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4525
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<pre style="margin: 0;">+<span id="LC4525" class="line" lang="c"> </span>
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<td class="diff-line-num new new_line" data-linenumber="4526" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4526
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<pre style="margin: 0;">+<span id="LC4526" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">exoni</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">nexons</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4527" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4527
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<pre style="margin: 0;">+<span id="LC4527" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"ABORTING BECAUSE OF EXONI %d >= NEXONS %d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">exoni</span><span class="p">,</span><span class="n" style="color: #333;">nexons</span><span class="p">));</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4528" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4528
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<pre style="margin: 0;">+<span id="LC4528" class="line" lang="c"> <span class="n" style="color: #333;">abortp</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4529" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4529
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<pre style="margin: 0;">+<span id="LC4529" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4530" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4530
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<pre style="margin: 0;">+<span id="LC4530" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"(16) exoni %d out of nexons %d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">exoni</span><span class="p">,</span><span class="n" style="color: #333;">nexons</span><span class="p">));</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4531" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4531
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<pre style="margin: 0;">+<span id="LC4531" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">exoni</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4532" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4532
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<pre style="margin: 0;">+<span id="LC4532" class="line" lang="c"> <span class="n" style="color: #333;">exonpos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">trstart</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4533" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4533
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<pre style="margin: 0;">+<span id="LC4533" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4534" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4534
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<pre style="margin: 0;">+<span id="LC4534" class="line" lang="c"> <span class="n" style="color: #333;">exonpos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">trstart</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">exonbounds</span><span class="p">[</span><span class="n" style="color: #333;">exoni</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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4535
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<pre style="margin: 0;">+<span id="LC4535" class="line" lang="c"> <span class="p">}</span></span>
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4536
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<pre style="margin: 0;">+<span id="LC4536" class="line" lang="c"> <span class="n" style="color: #333;">exon_residual</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">exonbounds</span><span class="p">[</span><span class="n" style="color: #333;">exoni</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">trstart</span><span class="p">;</span></span>
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4537
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<pre style="margin: 0;">+<span id="LC4537" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"exoni %d => exon_residual %d, exonpos %d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">exoni</span><span class="p">,</span><span class="n" style="color: #333;">exon_residual</span><span class="p">,</span><span class="n" style="color: #333;">exonpos</span><span class="p">));</span></span>
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4538
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<pre style="margin: 0;">+<span id="LC4538" class="line" lang="c"> </span>
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<td class="diff-line-num new new_line" data-linenumber="4539" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4539
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<pre style="margin: 0;">+<span id="LC4539" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Generate one substring per exon */</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4540" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4540
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<pre style="margin: 0;">+<span id="LC4540" class="line" lang="c"> <span class="n" style="color: #333;">genomicpos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">exonstarts</span><span class="p">[</span><span class="n" style="color: #333;">exoni</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">exonpos</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/* gminus */</span></span>
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4541
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<pre style="margin: 0;">+<span id="LC4541" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"genomicpos %u = %u - %u</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">genomicpos</span><span class="p">,</span><span class="n" style="color: #333;">exonstarts</span><span class="p">[</span><span class="n" style="color: #333;">exoni</span><span class="p">],</span><span class="n" style="color: #333;">exonpos</span><span class="p">));</span></span>
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4542
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<pre style="margin: 0;">+<span id="LC4542" class="line" lang="c"> <span class="n" style="color: #333;">align_residual</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">queryend</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">querystart</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4543" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4543
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<pre style="margin: 0;">+<span id="LC4543" class="line" lang="c"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">align_residual</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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4544
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<pre style="margin: 0;">+<span id="LC4544" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"abortp %d, align_residual %d, exon_residual %d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">abortp</span><span class="p">,</span><span class="n" style="color: #333;">align_residual</span><span class="p">,</span><span class="n" style="color: #333;">exon_residual</span><span class="p">));</span></span>
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4545
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<pre style="margin: 0;">+<span id="LC4545" class="line" lang="c"> <span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">align_residual</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">exon_residual</span><span class="p">)</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">align_residual</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">exon_residual</span><span class="p">;</span></span>
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4546
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<pre style="margin: 0;">+<span id="LC4546" class="line" lang="c"> <span class="n" style="color: #333;">querystart</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">queryend</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">len</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/* tminus */</span></span>
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4547
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<pre style="margin: 0;">+<span id="LC4547" class="line" lang="c"> </span>
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4548
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<pre style="margin: 0;">+<span id="LC4548" class="line" lang="c"> <span class="n" style="color: #333;">alignend</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">chroffset</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">genomicpos</span><span class="p">;</span></span>
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4549
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<pre style="margin: 0;">+<span id="LC4549" class="line" lang="c"> <span class="n" style="color: #333;">alignstart</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alignend</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">len</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/* gminus */</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4550" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4550
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<pre style="margin: 0;">+<span id="LC4550" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">left</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alignstart</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">querystart</span><span class="p">);</span> <span class="cm" style="color: #998; font-style: italic;">/* tminus == gminus */</span></span>
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4551
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<pre style="margin: 0;">+<span id="LC4551" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"tr ultrafast gap case 4 2nd part query %d..%d, align %u..%u [%u..%u], left %u = %u - %d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span></span>
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4552
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<pre style="margin: 0;">+<span id="LC4552" class="line" lang="c"> <span class="n" style="color: #333;">querystart</span><span class="p">,</span><span class="n" style="color: #333;">queryend</span><span class="p">,</span><span class="n" style="color: #333;">alignstart</span><span class="p">,</span><span class="n" style="color: #333;">alignend</span><span class="p">,</span><span class="n" style="color: #333;">alignstart</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">chroffset</span><span class="p">,</span><span class="n" style="color: #333;">alignend</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">chroffset</span><span class="p">,</span></span>
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4553
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<pre style="margin: 0;">+<span id="LC4553" class="line" lang="c"> <span class="n" style="color: #333;">left</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">chroffset</span><span class="p">,</span><span class="n" style="color: #333;">alignstart</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">chroffset</span><span class="p">,</span><span class="n" style="color: #333;">querystart</span><span class="p">));</span></span>
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4554
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<pre style="margin: 0;">+<span id="LC4554" class="line" lang="c"> </span>
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4555
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<pre style="margin: 0;">+<span id="LC4555" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* tminus: push alignend first */</span></span>
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4556
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<pre style="margin: 0;">+<span id="LC4556" class="line" lang="c"> <span class="n" style="color: #333;">endpoints</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Uintlist_push</span><span class="p">(</span><span class="n" style="color: #333;">endpoints</span><span class="p">,(</span><span class="n" style="color: #333;">Chrpos_T</span><span class="p">)</span> <span class="p">(</span><span class="n" style="color: #333;">alignend</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">chroffset</span><span class="p">));</span></span>
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4557
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<pre style="margin: 0;">+<span id="LC4557" class="line" lang="c"> <span class="n" style="color: #333;">endpoints</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Uintlist_push</span><span class="p">(</span><span class="n" style="color: #333;">endpoints</span><span class="p">,(</span><span class="n" style="color: #333;">Chrpos_T</span><span class="p">)</span> <span class="p">(</span><span class="n" style="color: #333;">alignstart</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">chroffset</span><span class="p">));</span></span>
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4558
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<pre style="margin: 0;">+<span id="LC4558" class="line" lang="c"> </span>
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4559
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<pre style="margin: 0;">+<span id="LC4559" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">align_residual</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">exon_residual</span><span class="p">)</span> <span class="p">{</span></span>
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4560
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<pre style="margin: 0;">+<span id="LC4560" class="line" lang="c"> <span class="n" style="color: #333;">exon_residual</span> <span class="o" style="font-weight: 600;">-=</span> <span class="n" style="color: #333;">align_residual</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/* Need to know this if we have a following deletion */</span></span>
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4561
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<pre style="margin: 0;">+<span id="LC4561" class="line" lang="c"> <span class="n" style="color: #333;">align_residual</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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4562
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<pre style="margin: 0;">+<span id="LC4562" class="line" lang="c"> <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="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">exoni</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">nexons</span><span class="p">)</span> <span class="p">{</span></span>
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4563
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<pre style="margin: 0;">+<span id="LC4563" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Aligning past the end of the transcript */</span></span>
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4564
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<pre style="margin: 0;">+<span id="LC4564" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"8 ABORTING BECAUSE ALIGNING PAST END OF TRANSCRIPT</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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4565
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<pre style="margin: 0;">+<span id="LC4565" class="line" lang="c"> <span class="n" style="color: #333;">align_residual</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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4511
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4566
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<pre style="margin: 0;"> <span id="LC4566" class="line" lang="c"> <span class="n" style="color: #333;">abortp</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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4512
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4567
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<pre style="margin: 0;"> <span id="LC4567" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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4513
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<td class="diff-line-num new_line old" data-linenumber="4568" 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="LC4513" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"(16) exoni %d out of nexons %d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">exoni</span><span class="p">,</span><span class="n" style="color: #333;">nexons</span><span class="p">));</span></span>
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4514
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<pre style="margin: 0;">-<span id="LC4514" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">exoni</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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4515
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<pre style="margin: 0;">-<span id="LC4515" class="line" lang="c"> <span class="n" style="color: #333;">exonpos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">trstart</span><span class="p">;</span></span>
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4516
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<pre style="margin: 0;">-<span id="LC4516" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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4517
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<pre style="margin: 0;">-<span id="LC4517" class="line" lang="c"> <span class="n" style="color: #333;">exonpos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">trstart</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">exonbounds</span><span class="p">[</span><span class="n" style="color: #333;">exoni</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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4518
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<pre style="margin: 0;">-<span id="LC4518" class="line" lang="c"> <span class="p">}</span></span>
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4519
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<pre style="margin: 0;">-<span id="LC4519" class="line" lang="c"> <span class="n" style="color: #333;">exon_residual</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">exonbounds</span><span class="p">[</span><span class="n" style="color: #333;">exoni</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">trstart</span><span class="p">;</span></span>
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4520
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<pre style="margin: 0;">-<span id="LC4520" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"exoni %d => exon_residual %d, exonpos %d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">exoni</span><span class="p">,</span><span class="n" style="color: #333;">exon_residual</span><span class="p">,</span><span class="n" style="color: #333;">exonpos</span><span class="p">));</span></span>
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4521
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<td class="diff-line-num new_line old" data-linenumber="4568" 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="LC4521" class="line" lang="c"></span>
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<td class="diff-line-num old old_line" data-linenumber="4522" 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">
4522
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<td class="diff-line-num new_line old" data-linenumber="4568" 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="LC4522" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Generate one substring per exon */</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4523" 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">
4523
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<td class="diff-line-num new_line old" data-linenumber="4568" 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="LC4523" class="line" lang="c"> <span class="n" style="color: #333;">genomicpos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">exonstarts</span><span class="p">[</span><span class="n" style="color: #333;">exoni</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">exonpos</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/* gminus */</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4524" 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">
4524
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<td class="diff-line-num new_line old" data-linenumber="4568" 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="LC4524" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"genomicpos %u = %u - %u</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">genomicpos</span><span class="p">,</span><span class="n" style="color: #333;">exonstarts</span><span class="p">[</span><span class="n" style="color: #333;">exoni</span><span class="p">],</span><span class="n" style="color: #333;">exonpos</span><span class="p">));</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4525" 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">
4525
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<td class="diff-line-num new_line old" data-linenumber="4568" 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="LC4525" class="line" lang="c"> <span class="n" style="color: #333;">align_residual</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">queryend</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">querystart</span><span class="p">;</span></span>
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4526
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<td class="diff-line-num new_line old" data-linenumber="4568" 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="LC4526" class="line" lang="c"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">align_residual</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4527" 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">
4527
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<td class="diff-line-num new_line old" data-linenumber="4568" 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="LC4527" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"abortp %d, align_residual %d, exon_residual %d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">abortp</span><span class="p">,</span><span class="n" style="color: #333;">align_residual</span><span class="p">,</span><span class="n" style="color: #333;">exon_residual</span><span class="p">));</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4528" 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">
4528
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<td class="diff-line-num new_line old" data-linenumber="4568" 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="LC4528" class="line" lang="c"> <span class="n" style="color: #333;">len</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">align_residual</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">exon_residual</span><span class="p">)</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">align_residual</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">exon_residual</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4529" 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">
4529
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<td class="diff-line-num new_line old" data-linenumber="4568" 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="LC4529" class="line" lang="c"> <span class="n" style="color: #333;">querystart</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">queryend</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">len</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/* tminus */</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4530" 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">
4530
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<td class="diff-line-num new_line old" data-linenumber="4568" 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="LC4530" class="line" lang="c"> </span>
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<td class="diff-line-num old old_line" data-linenumber="4531" 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">
4531
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<td class="diff-line-num new_line old" data-linenumber="4568" 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="LC4531" class="line" lang="c"> <span class="n" style="color: #333;">alignend</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">chroffset</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">genomicpos</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4532" 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">
4532
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<td class="diff-line-num new_line old" data-linenumber="4568" 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="LC4532" class="line" lang="c"> <span class="n" style="color: #333;">alignstart</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alignend</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">len</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/* gminus */</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4533" 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">
4533
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<td class="diff-line-num new_line old" data-linenumber="4568" 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="LC4533" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">left</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alignstart</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">querystart</span><span class="p">);</span> <span class="cm" style="color: #998; font-style: italic;">/* tminus == gminus */</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4534" 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">
4534
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<td class="diff-line-num new_line old" data-linenumber="4568" 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="LC4534" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"tr ultrafast gap case 4 2nd part query %d..%d, align %u..%u [%u..%u], left %u = %u - %d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4535" 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">
4535
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<td class="diff-line-num new_line old" data-linenumber="4568" 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="LC4535" class="line" lang="c"> <span class="n" style="color: #333;">querystart</span><span class="p">,</span><span class="n" style="color: #333;">queryend</span><span class="p">,</span><span class="n" style="color: #333;">alignstart</span><span class="p">,</span><span class="n" style="color: #333;">alignend</span><span class="p">,</span><span class="n" style="color: #333;">alignstart</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">chroffset</span><span class="p">,</span><span class="n" style="color: #333;">alignend</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">chroffset</span><span class="p">,</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4536" 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">
4536
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<td class="diff-line-num new_line old" data-linenumber="4568" 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="LC4536" class="line" lang="c"> <span class="n" style="color: #333;">left</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">chroffset</span><span class="p">,</span><span class="n" style="color: #333;">alignstart</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">chroffset</span><span class="p">,</span><span class="n" style="color: #333;">querystart</span><span class="p">));</span></span>
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4537
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<td class="diff-line-num new_line old" data-linenumber="4568" 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="LC4537" class="line" lang="c"></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="4538" 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">
4538
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<td class="diff-line-num new_line old" data-linenumber="4568" 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="LC4538" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* tminus: push alignend first */</span></span>
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4539
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<pre style="margin: 0;">-<span id="LC4539" class="line" lang="c"> <span class="n" style="color: #333;">endpoints</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Uintlist_push</span><span class="p">(</span><span class="n" style="color: #333;">endpoints</span><span class="p">,(</span><span class="n" style="color: #333;">Chrpos_T</span><span class="p">)</span> <span class="p">(</span><span class="n" style="color: #333;">alignend</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">chroffset</span><span class="p">));</span></span>
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4540
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<td class="diff-line-num new_line old" data-linenumber="4568" 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="LC4540" class="line" lang="c"> <span class="n" style="color: #333;">endpoints</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Uintlist_push</span><span class="p">(</span><span class="n" style="color: #333;">endpoints</span><span class="p">,(</span><span class="n" style="color: #333;">Chrpos_T</span><span class="p">)</span> <span class="p">(</span><span class="n" style="color: #333;">alignstart</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">chroffset</span><span class="p">));</span></span>
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4541
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<pre style="margin: 0;">-<span id="LC4541" class="line" lang="c"></span>
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4542
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<td class="diff-line-num new_line old" data-linenumber="4568" 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="LC4542" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">align_residual</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">exon_residual</span><span class="p">)</span> <span class="p">{</span></span>
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4543
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<td class="diff-line-num new_line old" data-linenumber="4568" 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="LC4543" class="line" lang="c"> <span class="n" style="color: #333;">exon_residual</span> <span class="o" style="font-weight: 600;">-=</span> <span class="n" style="color: #333;">align_residual</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/* Need to know this if we have a following deletion */</span></span>
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4544
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<td class="diff-line-num new_line old" data-linenumber="4568" 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="LC4544" class="line" lang="c"> <span class="n" style="color: #333;">align_residual</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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4545
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<td class="diff-line-num new_line old" data-linenumber="4568" 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="LC4545" class="line" lang="c"> <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="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">exoni</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">nexons</span><span class="p">)</span> <span class="p">{</span></span>
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4546
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<td class="diff-line-num new_line old" data-linenumber="4568" 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="LC4546" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Aligning past the end of the transcript */</span></span>
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4547
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<td class="diff-line-num new_line old" data-linenumber="4568" 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="LC4547" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"8 ABORTING BECAUSE ALIGNING PAST END OF TRANSCRIPT</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">));</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4548" 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">
4548
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<td class="diff-line-num new_line old" data-linenumber="4568" 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="LC4548" class="line" lang="c"> <span class="n" style="color: #333;">align_residual</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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4549
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<td class="diff-line-num new_line old" data-linenumber="4568" 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="LC4549" class="line" lang="c"> <span class="n" style="color: #333;">abortp</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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4550
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<pre style="margin: 0;">-<span id="LC4550" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4551" 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">
4551
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<td class="diff-line-num new_line old" data-linenumber="4568" 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="LC4551" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* nintrons += 1; */</span></span>
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4552
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<td class="diff-line-num new_line old" data-linenumber="4568" 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="LC4552" class="line" lang="c"> <span class="n" style="color: #333;">align_residual</span> <span class="o" style="font-weight: 600;">-=</span> <span class="n" style="color: #333;">len</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4553" 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">
4553
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<td class="diff-line-num new_line old" data-linenumber="4568" 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="LC4553" class="line" lang="c"> <span class="n" style="color: #333;">queryend</span> <span class="o" style="font-weight: 600;">-=</span> <span class="n" style="color: #333;">len</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/* tminus */</span></span>
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4554
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<td class="diff-line-num new_line old" data-linenumber="4568" 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="LC4554" class="line" lang="c"> <span class="n" style="color: #333;">genomicpos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">exonstarts</span><span class="p">[</span><span class="n" style="color: #333;">exoni</span><span class="p">];</span> <span class="cm" style="color: #998; font-style: italic;">/* gminus */</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4555" 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">
4555
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<td class="diff-line-num new_line old" data-linenumber="4568" 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="LC4555" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"genomicpos %u = %u</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">genomicpos</span><span class="p">,</span><span class="n" style="color: #333;">exonstarts</span><span class="p">[</span><span class="n" style="color: #333;">exoni</span><span class="p">]));</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4556" 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">
4556
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<td class="diff-line-num new_line old" data-linenumber="4568" 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="LC4556" class="line" lang="c"> <span class="n" style="color: #333;">exon_residual</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">exonbounds</span><span class="p">[</span><span class="n" style="color: #333;">exoni</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">exonbounds</span><span class="p">[</span><span class="n" style="color: #333;">exoni</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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4557
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<td class="diff-line-num new_line old" data-linenumber="4568" 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="LC4557" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"INTRON</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">));</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4558" 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">
4558
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<pre style="margin: 0;">-<span id="LC4558" class="line" lang="c"> <span class="n" style="color: #333;">gaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Intlist_push</span><span class="p">(</span><span class="n" style="color: #333;">gaps</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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4559
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<pre style="margin: 0;">-<span id="LC4559" class="line" lang="c"> <span class="p">}</span></span>
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4560
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<pre style="margin: 0;">-<span id="LC4560" class="line" lang="c"> <span class="p">}</span></span>
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4561
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<pre style="margin: 0;">-<span id="LC4561" class="line" lang="c"> <span class="p">}</span></span>
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4562
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<pre style="margin: 0;">-<span id="LC4562" class="line" lang="c"></span>
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4563
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<pre style="margin: 0;">-<span id="LC4563" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">abortp</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">)</span> <span class="p">{</span></span>
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4564
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<pre style="margin: 0;">-<span id="LC4564" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"ABORTING PATH</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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4565
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<pre style="margin: 0;">-<span id="LC4565" class="line" lang="c"> <span class="n" style="color: #333;">Uintlist_free</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">endpoints</span><span class="p">);</span></span>
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4566
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<pre style="margin: 0;">-<span id="LC4566" class="line" lang="c"> <span class="n" style="color: #333;">Intlist_free</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">gaps</span><span class="p">);</span></span>
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4567
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<pre style="margin: 0;">-<span id="LC4567" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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4568
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<td class="diff-line-num new_line old" data-linenumber="4568" 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="LC4568" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* gminus: Do not reverse endpoints or gaps */</span></span>
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4569
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<pre style="margin: 0;">-<span id="LC4569" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"PLUS PATH %d. ENDPOINTS: %s. GAPS: %s</span><span class="se" style="color: #d14;">\n\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span></span>
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4570
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<pre style="margin: 0;">-<span id="LC4570" class="line" lang="c"> <span class="n" style="color: #333;">ngplus</span><span class="p">,</span><span class="n" style="color: #333;">Uintlist_to_string</span><span class="p">(</span><span class="n" style="color: #333;">endpoints</span><span class="p">),</span><span class="n" style="color: #333;">Intlist_to_string</span><span class="p">(</span><span class="n" style="color: #333;">gaps</span><span class="p">)));</span></span>
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4571
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<pre style="margin: 0;">-<span id="LC4571" class="line" lang="c"> <span class="n" style="color: #333;">gplus_paths</span><span class="p">[</span><span class="n" style="color: #333;">ngplus</span><span class="o" style="font-weight: 600;">++</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Path_new</span><span class="p">(</span><span class="n" style="color: #333;">total_nmatches</span><span class="p">,</span><span class="n" style="color: #333;">trnum</span><span class="p">,</span><span class="n" style="color: #333;">overall_trend</span><span class="p">,</span><span class="n" style="color: #333;">overall_trstart</span><span class="p">,</span></span>
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4572
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<pre style="margin: 0;">-<span id="LC4572" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/*trim_low*/</span><span class="n" style="color: #333;">trim3</span><span class="p">,</span><span class="cm" style="color: #998; font-style: italic;">/*trim_high*/</span><span class="n" style="color: #333;">trim5</span><span class="p">,</span><span class="n" style="color: #333;">chrnum</span><span class="p">,</span><span class="n" style="color: #333;">chroffset</span><span class="p">,</span><span class="n" style="color: #333;">chrhigh</span><span class="p">,</span><span class="n" style="color: #333;">chrlength</span><span class="p">,</span></span>
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4573
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<pre style="margin: 0;">-<span id="LC4573" class="line" lang="c"> <span class="n" style="color: #333;">endpoints</span><span class="p">,</span><span class="n" style="color: #333;">gaps</span><span class="p">,</span><span class="n" style="color: #333;">concordantp</span><span class="p">);</span></span>
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4568
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<pre style="margin: 0;">+<span id="LC4568" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* nintrons += 1; */</span></span>
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4569
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<pre style="margin: 0;">+<span id="LC4569" class="line" lang="c"> <span class="n" style="color: #333;">align_residual</span> <span class="o" style="font-weight: 600;">-=</span> <span class="n" style="color: #333;">len</span><span class="p">;</span></span>
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4570
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<pre style="margin: 0;">+<span id="LC4570" class="line" lang="c"> <span class="n" style="color: #333;">queryend</span> <span class="o" style="font-weight: 600;">-=</span> <span class="n" style="color: #333;">len</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/* tminus */</span></span>
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4571
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<pre style="margin: 0;">+<span id="LC4571" class="line" lang="c"> <span class="n" style="color: #333;">genomicpos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">exonstarts</span><span class="p">[</span><span class="n" style="color: #333;">exoni</span><span class="p">];</span> <span class="cm" style="color: #998; font-style: italic;">/* gminus */</span></span>
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4572
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<pre style="margin: 0;">+<span id="LC4572" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"genomicpos %u = %u</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">genomicpos</span><span class="p">,</span><span class="n" style="color: #333;">exonstarts</span><span class="p">[</span><span class="n" style="color: #333;">exoni</span><span class="p">]));</span></span>
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4573
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<pre style="margin: 0;">+<span id="LC4573" class="line" lang="c"> <span class="n" style="color: #333;">exon_residual</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">exonbounds</span><span class="p">[</span><span class="n" style="color: #333;">exoni</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">exonbounds</span><span class="p">[</span><span class="n" style="color: #333;">exoni</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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4574
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<pre style="margin: 0;">+<span id="LC4574" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"INTRON</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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4575
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<pre style="margin: 0;">+<span id="LC4575" class="line" lang="c"> <span class="n" style="color: #333;">gaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Intlist_push</span><span class="p">(</span><span class="n" style="color: #333;">gaps</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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4574
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4576
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<pre style="margin: 0;"> <span id="LC4576" class="line" lang="c"> <span class="p">}</span></span>
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4575
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4577
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<pre style="margin: 0;"> <span id="LC4577" class="line" lang="c"> <span class="p">}</span></span>
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4576
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4578
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<pre style="margin: 0;"> <span id="LC4578" class="line" lang="c"> <span class="p">}</span></span>
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4579
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<pre style="margin: 0;">+<span id="LC4579" class="line" lang="c"> </span>
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4580
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<pre style="margin: 0;">+<span id="LC4580" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">abortp</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">)</span> <span class="p">{</span></span>
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4581
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<pre style="margin: 0;">+<span id="LC4581" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"ABORTING PATH</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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4582
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<pre style="margin: 0;">+<span id="LC4582" class="line" lang="c"> <span class="n" style="color: #333;">Uintlist_free</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">endpoints</span><span class="p">);</span></span>
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4583
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<pre style="margin: 0;">+<span id="LC4583" class="line" lang="c"> <span class="n" style="color: #333;">Intlist_free</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">gaps</span><span class="p">);</span></span>
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4584
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<pre style="margin: 0;">+<span id="LC4584" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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4585
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<pre style="margin: 0;">+<span id="LC4585" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* gminus: Do not reverse endpoints or gaps */</span></span>
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4586
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<pre style="margin: 0;">+<span id="LC4586" class="line" lang="c"> <span class="n" style="color: #333;">debug2</span><span class="p">(</span><span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"PLUS PATH %d. ENDPOINTS: %s. GAPS: %s</span><span class="se" style="color: #d14;">\n\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4587" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4587
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<pre style="margin: 0;">+<span id="LC4587" class="line" lang="c"> <span class="n" style="color: #333;">ngplus</span><span class="p">,</span><span class="n" style="color: #333;">Uintlist_to_string</span><span class="p">(</span><span class="n" style="color: #333;">endpoints</span><span class="p">),</span><span class="n" style="color: #333;">Intlist_to_string</span><span class="p">(</span><span class="n" style="color: #333;">gaps</span><span class="p">)));</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4588" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4588
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<pre style="margin: 0;">+<span id="LC4588" class="line" lang="c"> <span class="n" style="color: #333;">gplus_paths</span><span class="p">[</span><span class="n" style="color: #333;">ngplus</span><span class="o" style="font-weight: 600;">++</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Path_new</span><span class="p">(</span><span class="n" style="color: #333;">total_nmatches</span><span class="p">,</span><span class="n" style="color: #333;">trnum</span><span class="p">,</span><span class="n" style="color: #333;">overall_trend</span><span class="p">,</span><span class="n" style="color: #333;">overall_trstart</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4589" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4589
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<pre style="margin: 0;">+<span id="LC4589" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/*trim_low*/</span><span class="n" style="color: #333;">trim3</span><span class="p">,</span><span class="cm" style="color: #998; font-style: italic;">/*trim_high*/</span><span class="n" style="color: #333;">trim5</span><span class="p">,</span><span class="n" style="color: #333;">chrnum</span><span class="p">,</span><span class="n" style="color: #333;">chroffset</span><span class="p">,</span><span class="n" style="color: #333;">chrhigh</span><span class="p">,</span><span class="n" style="color: #333;">chrlength</span><span class="p">,</span></span>
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4590
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<pre style="margin: 0;">+<span id="LC4590" class="line" lang="c"> <span class="n" style="color: #333;">endpoints</span><span class="p">,</span><span class="n" style="color: #333;">gaps</span><span class="p">,</span><span class="n" style="color: #333;">concordantp</span><span class="p">);</span></span>
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4591
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<pre style="margin: 0;">+<span id="LC4591" class="line" lang="c"> <span class="p">}</span></span>
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4577
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4592
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<pre style="margin: 0;"> <span id="LC4592" class="line" lang="c"> <span class="p">}</span></span>
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4578
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4593
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<pre style="margin: 0;"> <span id="LC4593" class="line" lang="c"> <span class="p">}</span></span>
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4579
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<pre style="margin: 0;">-<span id="LC4579" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC4594" class="line" lang="c"> </span>
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4580
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4595
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<pre style="margin: 0;"> <span id="LC4595" class="line" lang="c"> <span class="n" style="color: #333;">FREE</span><span class="p">(</span><span class="n" style="color: #333;">tminus_diagpairs</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="4581" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4581
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<td class="diff-line-num new_line" data-linenumber="4596" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4596
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<pre style="margin: 0;"> <span id="LC4596" class="line" lang="c"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">tminus_gplus_paths</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gplus_paths</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="4582" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4582
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<td class="diff-line-num new_line" data-linenumber="4597" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4597
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<pre style="margin: 0;"> <span id="LC4597" class="line" lang="c"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">n_tminus_gplus</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ngplus</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4628" style="width: 35px; color: rgba(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="4643" style="width: 35px; color: rgba(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">@@ -4628,6 +4643,7 @@ Kmer_search_transcriptome_single (int *found_score_overall, int *found_score_wit</td>
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4628
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<td class="diff-line-num new_line" data-linenumber="4643" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4643
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<pre style="margin: 0;"> <span id="LC4643" class="line" lang="c"> <span class="n" style="color: #333;">query_compress_fwd</span><span class="p">,</span><span class="n" style="color: #333;">query_compress_rev</span><span class="p">,</span></span>
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<td class="diff-line-num old_line" data-linenumber="4629" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4629
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<td class="diff-line-num new_line" data-linenumber="4644" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4644
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<pre style="margin: 0;"> <span id="LC4644" class="line" lang="c"> <span class="n" style="color: #333;">transcript_iit</span><span class="p">,</span><span class="n" style="color: #333;">transcriptome</span><span class="p">,</span><span class="n" style="color: #333;">transcriptomebits</span><span class="p">,</span> </span>
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<td class="diff-line-num old_line" data-linenumber="4630" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4630
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<td class="diff-line-num new_line" data-linenumber="4645" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4645
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<pre style="margin: 0;"> <span id="LC4645" class="line" lang="c"> <span class="n" style="color: #333;">nmismatches_allowed</span><span class="p">,</span><span class="cm" style="color: #998; font-style: italic;">/*concordantp*/</span><span class="nb" style="color: #0086b3;">true</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new old_line" data-linenumber="4631" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="4646" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4646
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<pre style="margin: 0;">+<span id="LC4646" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Found hits */</span></span>
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4631
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<td class="diff-line-num new_line" data-linenumber="4647" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4647
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<pre style="margin: 0;"> <span id="LC4647" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="4632" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4632
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<td class="diff-line-num new_line" data-linenumber="4648" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4648
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<pre style="margin: 0;"> <span id="LC4648" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Will reassign paths from search_transcriptome_complete */</span></span>
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<td class="diff-line-num old_line" data-linenumber="4633" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4633
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4649
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<pre style="margin: 0;"> <span id="LC4649" class="line" lang="c"> <span class="n" style="color: #333;">FREE</span><span class="p">(</span><span class="n" style="color: #333;">tplus_gplus_paths</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4732" style="width: 35px; color: rgba(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="4748" style="width: 35px; color: rgba(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">@@ -4732,6 +4748,7 @@ Kmer_search_transcriptome_paired (int *found_score_5, int *found_score_3,</td>
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4732
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4748
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<pre style="margin: 0;"> <span id="LC4748" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> query5_compress_fwd,query5_compress_rev,</span></span>
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<td class="diff-line-num old_line" data-linenumber="4733" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4733
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<td class="diff-line-num new_line" data-linenumber="4749" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4749
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<pre style="margin: 0;"> <span id="LC4749" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> transcript_iit,transcriptome,transcriptomebits, </span></span>
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<td class="diff-line-num old_line" data-linenumber="4734" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4734
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<td class="diff-line-num new_line" data-linenumber="4750" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4750
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<pre style="margin: 0;"> <span id="LC4750" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> nmismatches_allowed_5,/*concordantp*/false) > 0) {</span></span>
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<td class="diff-line-num new old_line" data-linenumber="4735" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="4751" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4751
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<pre style="margin: 0;">+<span id="LC4751" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> /* Found hits */</span></span>
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4735
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<td class="diff-line-num new_line" data-linenumber="4752" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4752
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<pre style="margin: 0;"> <span id="LC4752" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> } else {</span></span>
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4736
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<td class="diff-line-num new_line" data-linenumber="4753" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4753
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<pre style="margin: 0;"> <span id="LC4753" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> /* Will reassign paths from search_transcriptome_complete */</span></span>
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<td class="diff-line-num old_line" data-linenumber="4737" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4737
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4754
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<pre style="margin: 0;"> <span id="LC4754" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> FREE(tplus_gplus_paths_5);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4774" style="width: 35px; color: rgba(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="4791" style="width: 35px; color: rgba(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">@@ -4774,6 +4791,7 @@ Kmer_search_transcriptome_paired (int *found_score_5, int *found_score_3,</td>
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4774
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4791
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<pre style="margin: 0;"> <span id="LC4791" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> query3_compress_fwd,query3_compress_rev,</span></span>
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4775
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4792
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<pre style="margin: 0;"> <span id="LC4792" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> transcript_iit,transcriptome,transcriptomebits, </span></span>
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4776
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4793
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<pre style="margin: 0;"> <span id="LC4793" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> nmismatches_allowed_3,/*concordantp*/false) > 0) {</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4794" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4794
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<pre style="margin: 0;">+<span id="LC4794" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> /* Found hits */</span></span>
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4777
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4795
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<pre style="margin: 0;"> <span id="LC4795" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> } else {</span></span>
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4778
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<td class="diff-line-num new_line" data-linenumber="4796" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4796
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<pre style="margin: 0;"> <span id="LC4796" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> /* Will reassign paths from search_transcriptome_complete */</span></span>
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<td class="diff-line-num old_line" data-linenumber="4779" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4779
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4797
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<pre style="margin: 0;"> <span id="LC4797" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> FREE(tplus_gplus_paths_3);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4857" style="width: 35px; color: rgba(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="4875" style="width: 35px; color: rgba(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">@@ -4857,6 +4875,7 @@ Kmer_search_transcriptome_paired (int *found_score_5, int *found_score_3,</td>
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4857
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4875
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<pre style="margin: 0;"> <span id="LC4875" class="line" lang="c"></span>
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4858
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4876
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<pre style="margin: 0;"> <span id="LC4876" class="line" lang="c"></span>
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4859
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<td class="diff-line-num new_line" data-linenumber="4877" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4877
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<pre style="margin: 0;"> <span id="LC4877" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/* Simplified from search_transcriptome_ends */</span></span>
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4878
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<pre style="margin: 0;">+<span id="LC4878" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/* Appears to be unused currently */</span></span>
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4860
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4879
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<pre style="margin: 0;"> <span id="LC4879" class="line" lang="c"><span class="n" style="color: #333;">List_T</span></span>
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4861
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4880
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<pre style="margin: 0;"> <span id="LC4880" class="line" lang="c"><span class="nf" style="color: #900; font-weight: 600;">Kmer_remap_transcriptome</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;">remap_sequence</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">remap_seqlength</span><span class="p">,</span> </span>
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4862
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4881
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<pre style="margin: 0;"> <span id="LC4881" class="line" lang="c"> <span class="n" style="color: #333;">Chrnum_T</span> <span class="n" style="color: #333;">chrnum</span><span class="p">,</span> <span class="n" style="color: #333;">Chrpos_T</span> <span class="n" style="color: #333;">lowbound</span><span class="p">,</span> <span class="n" style="color: #333;">Chrpos_T</span> <span class="n" style="color: #333;">highbound</span><span class="p">,</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="5232" style="width: 35px; color: rgba(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="5251" style="width: 35px; color: rgba(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">@@ -5232,6 +5251,7 @@ binary_search_univcoord (int lowi, int highi, Univcoord_T *positions, Univcoord_</td>
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5232
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5251
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<pre style="margin: 0;"> <span id="LC5251" class="line" lang="c"><span class="p">}</span></span>
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5233
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5252
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<pre style="margin: 0;"> <span id="LC5252" class="line" lang="c"></span>
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5234
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5253
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<pre style="margin: 0;"> <span id="LC5253" class="line" lang="c"></span>
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<td class="diff-line-num new new_line" data-linenumber="5254" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
5254
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<pre style="margin: 0;">+<span id="LC5254" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/* Genomic procedure */</span></span>
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5235
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5255
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<pre style="margin: 0;"> <span id="LC5255" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/* univdiagonal0/left0 is for the beginning of the query; univdiagonal1/left1 is for the end */</span></span>
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5236
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5256
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<pre style="margin: 0;"> <span id="LC5256" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/* Indel_resolve_middle_insertion is expecting left for the beginning of the query, or left0 */</span></span>
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5237
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5257
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<pre style="margin: 0;"> <span id="LC5257" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">void</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="5761" style="width: 35px; color: rgba(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="5781" style="width: 35px; color: rgba(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">@@ -5761,6 +5781,7 @@ combine_ends_plus (int *found_score_overall, int *found_score_within_trims,</td>
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5761
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5781
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<pre style="margin: 0;"> <span id="LC5781" class="line" lang="c"><span class="p">}</span></span>
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5762
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5782
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<pre style="margin: 0;"> <span id="LC5782" class="line" lang="c"></span>
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5763
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5783
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<pre style="margin: 0;"> <span id="LC5783" class="line" lang="c"></span>
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5784
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<pre style="margin: 0;">+<span id="LC5784" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/* Genomic procedure */</span></span>
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5764
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5785
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<pre style="margin: 0;"> <span id="LC5785" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/* left0 is for the beginning of the query; left1 is for the end */</span></span>
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5765
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5786
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<pre style="margin: 0;"> <span id="LC5786" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/* Indel_resolve_middle_insertion is expecting left for the beginning of the query, or left0 */</span></span>
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5766
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5787
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<pre style="margin: 0;"> <span id="LC5787" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">void</span></span>
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<a href="https://salsa.debian.org/med-team/gmap/-/compare/e36c478dd913ea44b8ccff832e1ed3c2409790ca...c42803c614bca47c818ce65af0a53b368a57e334#667933d29731aaedc5d4c17a05fe5bbc8d9cc3ef"><strong>src/pair.c</strong></a>
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1
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">rcsid</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"$Id: pair.c 223<span class="idiff left right">009 2020-07-10 15:13:26</span>Z twu $"</span><span class="p">;</span></span>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">rcsid</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"$Id: pair.c 223<span class="idiff left right">198 2020-10-15 22:24:59</span>Z twu $"</span><span class="p">;</span></span>
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2
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifdef HAVE_CONFIG_H</span></span>
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3
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <config.h></span></span>
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4
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -145,6 +145,7 @@ static bool novelsplicingp;</td>
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145
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<pre style="margin: 0;"> <span id="LC145" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="n" style="color: #333;">IIT_T</span> <span class="n" style="color: #333;">splicesites_iit</span><span class="p">;</span></span>
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146
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146
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<pre style="margin: 0;"> <span id="LC146" class="line" lang="c"></span>
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147
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<pre style="margin: 0;"> <span id="LC147" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">trim_indel_score</span><span class="p">;</span></span>
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148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">print_margin_p</span><span class="p">;</span></span>
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148
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149
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<pre style="margin: 0;"> <span id="LC149" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">gff3_separators_p</span><span class="p">;</span></span>
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149
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<pre style="margin: 0;"> <span id="LC150" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">sam_insert_0M_p</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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150
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<pre style="margin: 0;"> <span id="LC151" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">force_xs_direction_p</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="160" style="width: 35px; color: rgba(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">@@ -159,7 +160,8 @@ static Cigar_action_T cigar_action;</td>
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159
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160
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<pre style="margin: 0;"> <span id="LC160" class="line" lang="c"></span>
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160
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<pre style="margin: 0;"> <span id="LC161" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span></span>
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161
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<pre style="margin: 0;"> <span id="LC162" class="line" lang="c"><span class="nf" style="color: #900; font-weight: 600;">Pair_setup</span> <span class="p">(</span><span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">novelsplicingp_in</span><span class="p">,</span> <span class="n" style="color: #333;">IIT_T</span> <span class="n" style="color: #333;">splicesites_iit_in</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">trim_indel_score_in</span><span class="p">,</span></span>
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162
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<pre style="margin: 0;">-<span id="LC162" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">gff3_separators_p_in</span><span class="p">,</span> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">sam_insert_0M_p_in</span><span class="p">,</span> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">force_xs_direction_p_in</span><span class="p">,</span></span>
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163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">print_margin_p_in</span><span class="p">,</span> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">gff3_separators_p_in</span><span class="p">,</span></span>
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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">sam_insert_0M_p_in</span><span class="p">,</span> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">force_xs_direction_p_in</span><span class="p">,</span></span>
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163
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165
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<pre style="margin: 0;"> <span id="LC165" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">md_lowercase_variant_p_in</span><span class="p">,</span> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">snps_p_in</span><span class="p">,</span></span>
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164
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166
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<pre style="margin: 0;"> <span id="LC166" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">gff3_phase_swap_p_in</span><span class="p">,</span> <span class="n" style="color: #333;">CDStype_T</span> <span class="n" style="color: #333;">cdstype_in</span><span class="p">,</span></span>
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165
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167
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<pre style="margin: 0;"> <span id="LC167" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">cigar_extended_p_in</span><span class="p">,</span> <span class="n" style="color: #333;">Cigar_action_T</span> <span class="n" style="color: #333;">cigar_action_in</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="168" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="170" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -168,6 +170,7 @@ Pair_setup (bool novelsplicingp_in, IIT_T splicesites_iit_in, int trim_indel_sco</td>
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168
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170
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<pre style="margin: 0;"> <span id="LC170" class="line" lang="c"> <span class="n" style="color: #333;">splicesites_iit</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">splicesites_iit_in</span><span class="p">;</span></span>
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169
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171
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<pre style="margin: 0;"> <span id="LC171" class="line" lang="c"></span>
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170
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172
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<pre style="margin: 0;"> <span id="LC172" class="line" lang="c"> <span class="n" style="color: #333;">trim_indel_score</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">trim_indel_score_in</span><span class="p">;</span></span>
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173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="c"> <span class="n" style="color: #333;">print_margin_p</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">print_margin_p_in</span><span class="p">;</span></span>
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171
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174
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<pre style="margin: 0;"> <span id="LC174" class="line" lang="c"> <span class="n" style="color: #333;">gff3_separators_p</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gff3_separators_p_in</span><span class="p">;</span></span>
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172
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175
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<pre style="margin: 0;"> <span id="LC175" class="line" lang="c"> <span class="n" style="color: #333;">sam_insert_0M_p</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sam_insert_0M_p_in</span><span class="p">;</span></span>
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173
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176
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<pre style="margin: 0;"> <span id="LC176" class="line" lang="c"> <span class="n" style="color: #333;">force_xs_direction_p</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">force_xs_direction_p_in</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="572" style="width: 35px; color: rgba(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="575" style="width: 35px; color: rgba(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">@@ -572,19 +575,37 @@ Pair_protect_list (List_T pairs) {</td>
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572
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575
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<pre style="margin: 0;"> <span id="LC575" class="line" lang="c"><span class="k" style="font-weight: 600;">static</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;">RULER</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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573
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576
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<pre style="margin: 0;"> <span id="LC576" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">void</span></span>
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574
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577
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<pre style="margin: 0;"> <span id="LC577" class="line" lang="c"><span class="nf" style="color: #900; font-weight: 600;">print_top_ruler</span> <span class="p">(</span><span class="n" style="color: #333;">Filestring_T</span> <span class="n" style="color: #333;">fp</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">n</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">npairs</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">margin</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">wraplength</span><span class="p">)</span> <span class="p">{</span></span>
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575
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<pre style="margin: 0;">-<span id="LC575" class="line" lang="c"> <span class="n" style="color: #333;">FPRINTF</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">,</span><span class="s" style="color: #d14;">"%*d "</span><span class="p">,</span><span class="n" style="color: #333;">margin</span><span class="p">,</span><span class="n" style="color: #333;">n</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="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">wraplength</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">npairs</span><span class="p">)</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="c"> <span class="n" style="color: #333;">FPRINTF</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">,</span><span class="s" style="color: #d14;">"%s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">RULER</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="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">length</span><span class="p">,</span> <span class="n" style="color: #333;">i</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC579" class="line" lang="c"></span>
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580
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<pre style="margin: 0;">+<span id="LC580" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">npairs</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">wraplength</span><span class="p">)</span> <span class="p">{</span></span>
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581
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<pre style="margin: 0;">+<span id="LC581" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Complete line */</span></span>
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582
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<pre style="margin: 0;">+<span id="LC582" class="line" lang="c"> <span class="n" style="color: #333;">length</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">wraplength</span><span class="p">;</span></span>
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578
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583
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<pre style="margin: 0;"> <span id="LC583" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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579
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<td class="diff-line-num new_line old" data-linenumber="584" 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="LC579" class="line" lang="c"> <span class="n" style="color: #333;">FPRINTF</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">,</span><span class="s" style="color: #d14;">"%.*s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">npairs</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">n</span><span class="p">,</span><span class="n" style="color: #333;">RULER</span><span class="p">);</span></span>
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584
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<pre style="margin: 0;">+<span id="LC584" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Final line */</span></span>
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585
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<pre style="margin: 0;">+<span id="LC585" class="line" lang="c"> <span class="n" style="color: #333;">length</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">npairs</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">n</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="c"> <span class="p">}</span></span>
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587
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<pre style="margin: 0;">+<span id="LC587" class="line" lang="c"></span>
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588
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<pre style="margin: 0;">+<span id="LC588" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">print_margin_p</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">)</span> <span class="p">{</span></span>
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589
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<pre style="margin: 0;">+<span id="LC589" class="line" lang="c"> <span class="n" style="color: #333;">FPRINTF</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">,</span><span class="s" style="color: #d14;">"%*d "</span><span class="p">,</span><span class="n" style="color: #333;">margin</span><span class="p">,</span><span class="n" style="color: #333;">n</span><span class="p">);</span></span>
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580
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<pre style="margin: 0;"> <span id="LC590" class="line" lang="c"> <span class="p">}</span></span>
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591
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<pre style="margin: 0;">+<span id="LC591" class="line" lang="c"> <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>
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592
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<pre style="margin: 0;">+<span id="LC592" class="line" lang="c"> <span class="k" style="font-weight: 600;">while</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="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)</span> <span class="n" style="color: #333;">strlen</span><span class="p">(</span><span class="n" style="color: #333;">RULER</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">length</span><span class="p">)</span> <span class="p">{</span></span>
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593
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<pre style="margin: 0;">+<span id="LC593" class="line" lang="c"> <span class="n" style="color: #333;">FPRINTF</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">,</span><span class="s" style="color: #d14;">"%s"</span><span class="p">,</span><span class="n" style="color: #333;">RULER</span><span class="p">);</span></span>
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594
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<pre style="margin: 0;">+<span id="LC594" class="line" lang="c"> <span class="n" style="color: #333;">i</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;">strlen</span><span class="p">(</span><span class="n" style="color: #333;">RULER</span><span class="p">);</span></span>
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595
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<pre style="margin: 0;">+<span id="LC595" class="line" lang="c"> <span class="p">}</span></span>
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596
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<pre style="margin: 0;">+<span id="LC596" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">length</span><span class="p">)</span> <span class="p">{</span></span>
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597
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<pre style="margin: 0;">+<span id="LC597" class="line" lang="c"> <span class="n" style="color: #333;">FPRINTF</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">,</span><span class="s" style="color: #d14;">"%.*s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span><span class="n" style="color: #333;">length</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">i</span><span class="p">,</span><span class="n" style="color: #333;">RULER</span><span class="p">);</span></span>
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598
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<pre style="margin: 0;">+<span id="LC598" class="line" lang="c"> <span class="p">}</span></span>
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599
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<pre style="margin: 0;">+<span id="LC599" class="line" lang="c"></span>
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600
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<pre style="margin: 0;"> <span id="LC600" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>
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601
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<pre style="margin: 0;"> <span id="LC601" class="line" lang="c"><span class="p">}</span></span>
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602
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<pre style="margin: 0;"> <span id="LC602" class="line" lang="c"></span>
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603
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<pre style="margin: 0;"> <span id="LC603" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/*</span></span>
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585
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604
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<pre style="margin: 0;"> <span id="LC604" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">static void</span></span>
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586
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605
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<pre style="margin: 0;"> <span id="LC605" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">print_bottom_ruler (int n, int npairs, int margin, int wraplength) {</span></span>
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587
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<pre style="margin: 0;">-<span id="LC587" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> printf("%*s ",margin,"");</span></span>
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606
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<pre style="margin: 0;">+<span id="LC606" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> if (print_margin_p == true) {</span></span>
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<pre style="margin: 0;">+<span id="LC607" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> printf("%*s ",margin,"");</span></span>
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608
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<pre style="margin: 0;">+<span id="LC608" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> }</span></span>
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609
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<pre style="margin: 0;"> <span id="LC609" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> if (n + wraplength < npairs) {</span></span>
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610
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<pre style="margin: 0;"> <span id="LC610" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> printf("%s\n",RULER);</span></span>
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<pre style="margin: 0;"> <span id="LC611" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> } else {</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">@@ -601,7 +622,9 @@ print_cdna_sequence (Filestring_T fp, struct T *ptr, int n, int npairs, int marg</td>
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<pre style="margin: 0;"> <span id="LC622" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC623" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC624" class="line" lang="c"> <span class="n" style="color: #333;">this</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ptr</span><span class="p">;</span></span>
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604
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<pre style="margin: 0;">-<span id="LC604" class="line" lang="c"> <span class="n" style="color: #333;">FPRINTF</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">,</span><span class="s" style="color: #d14;">"%*u "</span><span class="p">,</span><span class="n" style="color: #333;">margin</span><span class="p">,</span><span class="n" style="color: #333;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">querypos</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">ONEBASEDP</span><span class="p">);</span></span>
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625
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<pre style="margin: 0;">+<span id="LC625" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">print_margin_p</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">)</span> <span class="p">{</span></span>
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626
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<pre style="margin: 0;">+<span id="LC626" class="line" lang="c"> <span class="n" style="color: #333;">FPRINTF</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">,</span><span class="s" style="color: #d14;">"%*u "</span><span class="p">,</span><span class="n" style="color: #333;">margin</span><span class="p">,</span><span class="n" style="color: #333;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">querypos</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">ONEBASEDP</span><span class="p">);</span></span>
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627
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<pre style="margin: 0;">+<span id="LC627" class="line" lang="c"> <span class="p">}</span></span>
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605
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628
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<pre style="margin: 0;"> <span id="LC628" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">npairs</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">wraplength</span><span class="p">;</span> <span class="n" style="color: #333;">n</span><span class="o" style="font-weight: 600;">++</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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606
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629
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<pre style="margin: 0;"> <span id="LC629" class="line" lang="c"> <span class="n" style="color: #333;">this</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ptr</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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630
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<pre style="margin: 0;"> <span id="LC630" class="line" lang="c"> <span class="n" style="color: #333;">PUTC</span><span class="p">(</span><span class="n" style="color: #333;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">cdna</span><span class="p">,</span><span class="n" style="color: #333;">fp</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">@@ -640,7 +663,9 @@ print_peptide (Filestring_T fp, struct T *ptr, int n, int npairs, int margin,</td>
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663
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<pre style="margin: 0;"> <span id="LC663" class="line" lang="c"> <span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">T</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">this</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC664" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">aapos</span><span class="p">,</span> <span class="n" style="color: #333;">i</span><span class="p">;</span></span>
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665
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<pre style="margin: 0;"> <span id="LC665" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC643" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">aapos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">find_aapos_in_line</span><span class="p">(</span><span class="n" style="color: #333;">ptr</span><span class="p">,</span><span class="n" style="color: #333;">n</span><span class="p">,</span><span class="n" style="color: #333;">npairs</span><span class="p">,</span><span class="n" style="color: #333;">wraplength</span><span class="p">,</span><span class="n" style="color: #333;">genomep</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="LC666" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">print_margin_p</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC667" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Skip */</span></span>
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<pre style="margin: 0;">+<span id="LC668" class="line" lang="c"> <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;">aapos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">find_aapos_in_line</span><span class="p">(</span><span class="n" style="color: #333;">ptr</span><span class="p">,</span><span class="n" style="color: #333;">n</span><span class="p">,</span><span class="n" style="color: #333;">npairs</span><span class="p">,</span><span class="n" style="color: #333;">wraplength</span><span class="p">,</span><span class="n" style="color: #333;">genomep</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="LC669" class="line" lang="c"> <span class="n" style="color: #333;">FPRINTF</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">,</span><span class="s" style="color: #d14;">"%*s "</span><span class="p">,</span><span class="n" style="color: #333;">margin</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="LC670" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC671" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* 4 is length of "aa.c" and "aa.g" */</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">@@ -673,7 +698,9 @@ print_alignment (Filestring_T fp, struct T *ptr, int n, int npairs,</td>
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<pre style="margin: 0;"> <span id="LC698" class="line" lang="c"> <span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">T</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">this</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC699" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC700" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC676" class="line" lang="c"> <span class="n" style="color: #333;">FPRINTF</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">,</span><span class="s" style="color: #d14;">"%*s "</span><span class="p">,</span><span class="n" style="color: #333;">margin</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="LC701" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">print_margin_p</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC702" class="line" lang="c"> <span class="n" style="color: #333;">FPRINTF</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">,</span><span class="s" style="color: #d14;">"%*s "</span><span class="p">,</span><span class="n" style="color: #333;">margin</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="LC703" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC704" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">npairs</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">wraplength</span><span class="p">;</span> <span class="n" style="color: #333;">n</span><span class="o" style="font-weight: 600;">++</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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705
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<pre style="margin: 0;"> <span id="LC705" class="line" lang="c"> <span class="n" style="color: #333;">this</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ptr</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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679
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706
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<pre style="margin: 0;"> <span id="LC706" class="line" lang="c"> </span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="756" style="width: 35px; color: rgba(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">@@ -729,7 +756,9 @@ print_genomic_sequence (Filestring_T fp, struct T *ptr, int n, int npairs,</td>
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729
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756
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<pre style="margin: 0;"> <span id="LC756" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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730
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757
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<pre style="margin: 0;"> <span id="LC757" class="line" lang="c"> <span class="n" style="color: #333;">sprintf</span><span class="p">(</span><span class="n" style="color: #333;">Buffer</span><span class="p">,</span><span class="s" style="color: #d14;">"%s:%llu"</span><span class="p">,</span><span class="n" style="color: #333;">chrstring</span><span class="p">,(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">long</span><span class="p">)</span> <span class="p">(</span><span class="n" style="color: #333;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">genomepos</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">ONEBASEDP</span><span class="p">));</span></span>
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731
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758
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<pre style="margin: 0;"> <span id="LC758" class="line" lang="c"> <span class="p">}</span></span>
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732
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<pre style="margin: 0;">-<span id="LC732" class="line" lang="c"> <span class="n" style="color: #333;">FPRINTF</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">,</span><span class="s" style="color: #d14;">"%*s "</span><span class="p">,</span><span class="n" style="color: #333;">margin</span><span class="p">,</span><span class="n" style="color: #333;">Buffer</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="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">print_margin_p</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">)</span> <span class="p">{</span></span>
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760
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<pre style="margin: 0;">+<span id="LC760" class="line" lang="c"> <span class="n" style="color: #333;">FPRINTF</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">,</span><span class="s" style="color: #d14;">"%*s "</span><span class="p">,</span><span class="n" style="color: #333;">margin</span><span class="p">,</span><span class="n" style="color: #333;">Buffer</span><span class="p">);</span></span>
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761
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<pre style="margin: 0;">+<span id="LC761" class="line" lang="c"> <span class="p">}</span></span>
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733
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762
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<pre style="margin: 0;"> <span id="LC762" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">npairs</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">wraplength</span><span class="p">;</span> <span class="n" style="color: #333;">n</span><span class="o" style="font-weight: 600;">++</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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734
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763
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<pre style="margin: 0;"> <span id="LC763" class="line" lang="c"> <span class="n" style="color: #333;">this</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ptr</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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764
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<pre style="margin: 0;"> <span id="LC764" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">comp</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">EXTRAEXON_COMP</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="756" style="width: 35px; color: rgba(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="785" style="width: 35px; color: rgba(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">@@ -756,7 +785,9 @@ print_genomicalt_sequence (Filestring_T fp, struct T *ptr, int n, int npairs,</td>
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756
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785
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<pre style="margin: 0;"> <span id="LC785" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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757
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786
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<pre style="margin: 0;"> <span id="LC786" class="line" lang="c"> <span class="n" style="color: #333;">sprintf</span><span class="p">(</span><span class="n" style="color: #333;">Buffer</span><span class="p">,</span><span class="s" style="color: #d14;">"%s:%llu"</span><span class="p">,</span><span class="n" style="color: #333;">chrstring</span><span class="p">,</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">long</span><span class="p">)</span> <span class="p">(</span><span class="n" style="color: #333;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">genomepos</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">ONEBASEDP</span><span class="p">));</span></span>
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758
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787
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<pre style="margin: 0;"> <span id="LC787" class="line" lang="c"> <span class="p">}</span></span>
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759
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<pre style="margin: 0;">-<span id="LC759" class="line" lang="c"> <span class="n" style="color: #333;">FPRINTF</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">,</span><span class="s" style="color: #d14;">"%*s "</span><span class="p">,</span><span class="n" style="color: #333;">margin</span><span class="p">,</span><span class="n" style="color: #333;">Buffer</span><span class="p">);</span></span>
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788
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<pre style="margin: 0;">+<span id="LC788" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">print_margin_p</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC789" class="line" lang="c"> <span class="n" style="color: #333;">FPRINTF</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">,</span><span class="s" style="color: #d14;">"%*s "</span><span class="p">,</span><span class="n" style="color: #333;">margin</span><span class="p">,</span><span class="n" style="color: #333;">Buffer</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC790" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC791" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">npairs</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">wraplength</span><span class="p">;</span> <span class="n" style="color: #333;">n</span><span class="o" style="font-weight: 600;">++</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="LC792" class="line" lang="c"> <span class="n" style="color: #333;">this</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ptr</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC793" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">comp</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">EXTRAEXON_COMP</span><span class="p">)</span> <span class="p">{</span></span>
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<a href="https://salsa.debian.org/med-team/gmap/-/compare/e36c478dd913ea44b8ccff832e1ed3c2409790ca...c42803c614bca47c818ce65af0a53b368a57e334#d6ba69bc1ae89700307c00a3b1afeef776cfb00a"><strong>src/pair.h</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/* $Id: pair.h 22<span class="idiff left right">2194 2020-03-23 13:44:44</span>Z twu $ */</span></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/* $Id: pair.h 22<span class="idiff left right">3198 2020-10-15 22:24:59</span>Z twu $ */</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifndef PAIR_INCLUDED</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define PAIR_INCLUDED</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="c"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -29,7 +29,8 @@ typedef enum {CIGAR_ACTION_IGNORE, CIGAR_ACTION_WARNING, CIGAR_ACTION_NOPRINT, C</td>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="c"><span class="k" style="font-weight: 600;">extern</span> <span class="kt" style="color: #458; font-weight: 600;">void</span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="c"><span class="nf" style="color: #900; font-weight: 600;">Pair_setup</span> <span class="p">(</span><span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">novelsplicingp_in</span><span class="p">,</span> <span class="n" style="color: #333;">IIT_T</span> <span class="n" style="color: #333;">splicesites_iit_in</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">trim_indel_score_in</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">gff3_separators_p_in</span><span class="p">,</span> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">sam_insert_0M_p_in</span><span class="p">,</span> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">force_xs_direction_p_in</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">print_margin_p_in</span><span class="p">,</span> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">gff3_separators_p_in</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">sam_insert_0M_p_in</span><span class="p">,</span> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">force_xs_direction_p_in</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">md_lowercase_variant_p_in</span><span class="p">,</span> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">snps_p_in</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">gff3_phase_swap_p_in</span><span class="p">,</span> <span class="n" style="color: #333;">CDStype_T</span> <span class="n" style="color: #333;">cdstype_in</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">cigar_extended_p_in</span><span class="p">,</span> <span class="n" style="color: #333;">Cigar_action_T</span> <span class="n" style="color: #333;">cigar_action_in</span><span class="p">);</span></span>
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<a href="https://salsa.debian.org/med-team/gmap/-/compare/e36c478dd913ea44b8ccff832e1ed3c2409790ca...c42803c614bca47c818ce65af0a53b368a57e334#2d331dd15dccff926559b191048c3a7d2d3a5fae"><strong>src/stage3hr.c</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="">static char rcsid[] = "$Id: stage3hr.c 223<span class="idiff left right">081 2020-09-13 14:21:0</span>3Z twu $";</span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="">static char rcsid[] = "$Id: stage3hr.c 223<span class="idiff left right">176 2020-10-15 01:51:2</span>3Z twu $";</span>
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="">#ifdef HAVE_CONFIG_H</span>
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="">#include <config.h></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="">#endif</span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="173" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -173,6 +173,7 @@ static char rcsid[] = "$Id: stage3hr.c 223081 2020-09-13 14:21:03Z twu $";</td>
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173
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173
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<pre style="margin: 0;"> <span id="LC173" class="line" lang=""></span>
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174
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<pre style="margin: 0;"> <span id="LC174" class="line" lang=""></span>
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<pre style="margin: 0;"> <span id="LC175" class="line" lang="">#define MAPQ_MAXIMUM_SCORE 40</span>
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="">/* #define REMAP_TRANSCRIPTOME */</span>
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<pre style="margin: 0;"> <span id="LC177" class="line" lang=""></span>
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<pre style="margin: 0;"> <span id="LC178" class="line" lang="">static bool omit_concordant_uniq_p = false;</span>
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<pre style="margin: 0;"> <span id="LC179" class="line" lang="">static bool omit_concordant_mult_p = false;</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">@@ -197,7 +198,6 @@ static int circular_typeint;</td>
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<pre style="margin: 0;"> <span id="LC198" class="line" lang="">static Genome_T transcriptomebits;</span>
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<pre style="margin: 0;"> <span id="LC199" class="line" lang="">static Transcriptome_T transcriptome;</span>
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<pre style="margin: 0;"> <span id="LC200" class="line" lang="">static Univ_IIT_T transcript_iit;</span>
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<pre style="margin: 0;">-<span id="LC200" class="line" lang="">static bool remap_transcriptome_p = false;</span>
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<pre style="margin: 0;"> <span id="LC201" class="line" lang=""></span>
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<pre style="margin: 0;"> <span id="LC202" class="line" lang="">static IIT_T tally_iit;</span>
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<pre style="margin: 0;"> <span id="LC203" class="line" lang="">static int *tally_divint_crosstable;</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">@@ -3782,7 +3782,7 @@ Stage3end_new_precomputed (int *found_score_overall, int *found_score_within_tri</td>
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3782
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3782
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<pre style="margin: 0;"> <span id="LC3782" class="line" lang=""></span>
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3783
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3783
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<pre style="margin: 0;"> <span id="LC3783" class="line" lang=""></span>
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3784
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3784
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<pre style="margin: 0;"> <span id="LC3784" class="line" lang="">#ifdef DEBUG0</span>
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3785
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<pre style="margin: 0;">-<span id="LC3785" class="line" lang=""> printf("NEW SUBSTRINGS (query order)\n");</span>
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3785
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<pre style="margin: 0;">+<span id="LC3785" class="line" lang=""> printf("NEW SUBSTRINGS (query order)<span class="idiff left right"> (1)</span>\n");</span>
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3786
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3786
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<pre style="margin: 0;"> <span id="LC3786" class="line" lang=""> for (p = new->substrings_1toN; p != NULL; p = List_next(p)) {</span>
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3787
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3787
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<pre style="margin: 0;"> <span id="LC3787" class="line" lang=""> substring = List_head(p);</span>
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3788
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3788
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<pre style="margin: 0;"> <span id="LC3788" class="line" lang=""> if (Substring_ambiguous_p(substring) == true) {</span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="5468" style="width: 35px; color: rgba(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">@@ -5468,7 +5468,7 @@ Stage3end_new_splice (int *found_score_overall, int *found_score_within_trims,</td>
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5468
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5468
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<pre style="margin: 0;"> <span id="LC5468" class="line" lang=""> }</span>
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5469
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5469
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<pre style="margin: 0;"> <span id="LC5469" class="line" lang=""></span>
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5470
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5470
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<pre style="margin: 0;"> <span id="LC5470" class="line" lang="">#ifdef DEBUG0</span>
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5471
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<pre style="margin: 0;">-<span id="LC5471" class="line" lang=""> printf("NEW SUBSTRINGS (query order)\n");</span>
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5471
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<pre style="margin: 0;">+<span id="LC5471" class="line" lang=""> printf("NEW SUBSTRINGS (query order)<span class="idiff left right"> (2)</span>\n");</span>
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5472
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5472
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<pre style="margin: 0;"> <span id="LC5472" class="line" lang=""> for (p = new->substrings_1toN; p != NULL; p = List_next(p)) {</span>
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5473
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5473
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<pre style="margin: 0;"> <span id="LC5473" class="line" lang=""> substring = List_head(p);</span>
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5474
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5474
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<pre style="margin: 0;"> <span id="LC5474" class="line" lang=""> if (Substring_ambiguous_p(substring) == true) {</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="5570" style="width: 35px; color: rgba(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="5570" style="width: 35px; color: rgba(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">@@ -5570,7 +5570,8 @@ Stage3end_new_splice (int *found_score_overall, int *found_score_within_trims,</td>
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5570
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5570
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<pre style="margin: 0;"> <span id="LC5570" class="line" lang=""> } else {</span>
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5571
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5571
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<pre style="margin: 0;"> <span id="LC5571" class="line" lang=""> }</span>
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5572
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5572
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<pre style="margin: 0;"> <span id="LC5572" class="line" lang=""> </span>
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5573
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<pre style="margin: 0;">-<span id="LC5573" class="line" lang=""> if (transcriptomep == true && remap_transcriptome_p == true && substring_for_concordance != NULL) {</span>
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5573
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<pre style="margin: 0;">+<span id="LC5573" class="line" lang="">#ifdef REMAP_TRANSCRIPTOME</span>
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5574
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<pre style="margin: 0;">+<span id="LC5574" class="line" lang=""> if (transcriptomep == true && substring_for_concordance != NULL) {</span>
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5574
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5575
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<pre style="margin: 0;"> <span id="LC5575" class="line" lang=""> /* Remap substring_for_concordance */</span>
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5575
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5576
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<pre style="margin: 0;"> <span id="LC5576" class="line" lang=""> remap_sequence = Substring_genomic_sequence(&remap_seqlength,substring_for_concordance,genomecomp);</span>
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5576
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5577
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<pre style="margin: 0;"> <span id="LC5577" class="line" lang=""> if ((transcripts = Kmer_remap_transcriptome(remap_sequence,remap_seqlength,new->effective_chrnum,</span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="5592" style="width: 35px; color: rgba(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">@@ -5591,6 +5592,7 @@ Stage3end_new_splice (int *found_score_overall, int *found_score_within_trims,</td>
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5591
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5592
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<pre style="margin: 0;"> <span id="LC5592" class="line" lang=""> }</span>
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5592
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5593
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<pre style="margin: 0;"> <span id="LC5593" class="line" lang=""> FREE(remap_sequence);</span>
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5593
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5594
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<pre style="margin: 0;"> <span id="LC5594" class="line" lang=""> }</span>
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5595
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<pre style="margin: 0;">+<span id="LC5595" class="line" lang="">#endif</span>
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5594
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5596
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<pre style="margin: 0;"> <span id="LC5596" class="line" lang=""> </span>
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5595
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5597
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<pre style="margin: 0;"> <span id="LC5597" class="line" lang=""> debug0(printf("*****Method %s: Returning new splice %p at genomic %u..%u, donor %p (%u => %u), acceptor %p (%u => %u), score %d\n\n",</span>
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5596
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5598
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<pre style="margin: 0;"> <span id="LC5598" class="line" lang=""> Method_string(method),new,new->genomicstart - new->chroffset,new->genomicend - new->chroffset,donor,</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="5771" style="width: 35px; color: rgba(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="5773" style="width: 35px; color: rgba(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">@@ -5771,7 +5773,7 @@ Stage3end_new_distant (int *found_score_overall, int *found_score_within_trims,</td>
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5771
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5773
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<pre style="margin: 0;"> <span id="LC5773" class="line" lang=""> new->plusp = Substring_plusp(substring_for_concordance);</span>
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5772
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5774
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<pre style="margin: 0;"> <span id="LC5774" class="line" lang=""> </span>
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5773
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5775
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<pre style="margin: 0;"> <span id="LC5775" class="line" lang="">#ifdef DEBUG0</span>
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5774
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<pre style="margin: 0;">-<span id="LC5774" class="line" lang=""> printf("NEW SUBSTRINGS (query order)\n");</span>
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5776
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<pre style="margin: 0;">+<span id="LC5776" class="line" lang=""> printf("NEW SUBSTRINGS (query order)<span class="idiff left right"> (3)</span>\n");</span>
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5775
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5777
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<pre style="margin: 0;"> <span id="LC5777" class="line" lang=""> for (p = new->substrings_1toN; p != NULL; p = List_next(p)) {</span>
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5776
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5778
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<pre style="margin: 0;"> <span id="LC5778" class="line" lang=""> substring = List_head(p);</span>
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5777
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5779
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<pre style="margin: 0;"> <span id="LC5779" class="line" lang=""> if (Substring_ambiguous_p(substring) == true) {</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="5862" style="width: 35px; color: rgba(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="5864" style="width: 35px; color: rgba(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">@@ -5862,7 +5864,8 @@ Stage3end_new_distant (int *found_score_overall, int *found_score_within_trims,</td>
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5862
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5864
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<pre style="margin: 0;"> <span id="LC5864" class="line" lang=""> } else {</span>
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5863
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5865
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<pre style="margin: 0;"> <span id="LC5865" class="line" lang=""> }</span>
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5864
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5866
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<pre style="margin: 0;"> <span id="LC5866" class="line" lang=""> </span>
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5865
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<pre style="margin: 0;">-<span id="LC5865" class="line" lang=""> if (transcriptomep == true && remap_transcriptome_p == true && substring_for_concordance != NULL) {</span>
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5867
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<pre style="margin: 0;">+<span id="LC5867" class="line" lang="">#ifdef REMAP_TRANSCRIPTOME</span>
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5868
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<pre style="margin: 0;">+<span id="LC5868" class="line" lang=""> if (transcriptomep == true && substring_for_concordance != NULL) {</span>
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5866
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5869
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<pre style="margin: 0;"> <span id="LC5869" class="line" lang=""> /* Remap substring_for_concordance */</span>
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5867
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5870
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<pre style="margin: 0;"> <span id="LC5870" class="line" lang=""> remap_sequence = Substring_genomic_sequence(&remap_seqlength,substring_for_concordance,genomecomp);</span>
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5868
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5871
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<pre style="margin: 0;"> <span id="LC5871" class="line" lang=""> if ((transcripts = Kmer_remap_transcriptome(remap_sequence,remap_seqlength,new->effective_chrnum,</span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="5886" style="width: 35px; color: rgba(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">@@ -5883,6 +5886,7 @@ Stage3end_new_distant (int *found_score_overall, int *found_score_within_trims,</td>
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5883
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5886
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<pre style="margin: 0;"> <span id="LC5886" class="line" lang=""> }</span>
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5884
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5887
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<pre style="margin: 0;"> <span id="LC5887" class="line" lang=""> FREE(remap_sequence);</span>
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5885
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5888
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<pre style="margin: 0;"> <span id="LC5888" class="line" lang=""> }</span>
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5889
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<pre style="margin: 0;">+<span id="LC5889" class="line" lang="">#endif</span>
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5886
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5890
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<pre style="margin: 0;"> <span id="LC5890" class="line" lang=""> </span>
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5887
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5891
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<pre style="margin: 0;"> <span id="LC5891" class="line" lang=""> debug0(printf("*****Method distant: Returning new distant %p at genomic %u..%u, startfrag %p (%u => ), endfrag %p (%u => ), score %d\n\n",</span>
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5888
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5892
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<pre style="margin: 0;"> <span id="LC5892" class="line" lang=""> new,new->genomicstart - new->chroffset,new->genomicend - new->chroffset,</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="11802" style="width: 35px; color: rgba(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="11806" style="width: 35px; color: rgba(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">@@ -11802,10 +11806,8 @@ Stage3pair_new (T hit5_orig, T hit3_orig, int genestrand, int sensedir, Pairtype</td>
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11802
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11806
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<pre style="margin: 0;"> <span id="LC11806" class="line" lang=""> unalias_circular(hit3);</span>
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11803
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11807
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<pre style="margin: 0;"> <span id="LC11807" class="line" lang=""> }</span>
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11804
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11808
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<pre style="margin: 0;"> <span id="LC11808" class="line" lang=""></span>
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11805
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<pre style="margin: 0;">-<span id="LC11805" class="line" lang=""> if (remap_transcriptome_p == false) {</span>
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11806
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<pre style="margin: 0;">-<span id="LC11806" class="line" lang=""> /* Do not remap */</span>
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11807
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<pre style="margin: 0;">-<span id="LC11807" class="line" lang=""></span>
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11808
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<pre style="margin: 0;">-<span id="LC11808" class="line" lang=""> } else if (hit5->transcripts != NULL && hit3->transcripts != NULL) {</span>
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<pre style="margin: 0;">+<span id="LC11809" class="line" lang="">#ifdef REMAP_TRANSCRIPTOME</span>
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11810
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<pre style="margin: 0;">+<span id="LC11810" class="line" lang=""> if (hit5->transcripts != NULL && hit3->transcripts != NULL) {</span>
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11809
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11811
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<pre style="margin: 0;"> <span id="LC11811" class="line" lang=""> /* No need to remap */</span>
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11810
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11812
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<pre style="margin: 0;"> <span id="LC11812" class="line" lang=""></span>
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11811
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11813
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<pre style="margin: 0;"> <span id="LC11813" class="line" lang=""> } else if (hit5->transcripts != NULL && hit3->transcripts == NULL) {</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="11836" style="width: 35px; color: rgba(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="11838" style="width: 35px; color: rgba(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">@@ -11836,6 +11838,7 @@ Stage3pair_new (T hit5_orig, T hit3_orig, int genestrand, int sensedir, Pairtype</td>
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11836
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11838
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<pre style="margin: 0;"> <span id="LC11838" class="line" lang=""> }</span>
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11837
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11839
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<pre style="margin: 0;"> <span id="LC11839" class="line" lang=""> FREE(remap_sequence);</span>
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11838
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11840
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<pre style="margin: 0;"> <span id="LC11840" class="line" lang=""> }</span>
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11841
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<pre style="margin: 0;">+<span id="LC11841" class="line" lang="">#endif</span>
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11839
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11842
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<pre style="margin: 0;"> <span id="LC11842" class="line" lang=""></span>
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11840
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11843
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<pre style="margin: 0;"> <span id="LC11843" class="line" lang="">#if 0</span>
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11841
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11844
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<pre style="margin: 0;"> <span id="LC11844" class="line" lang=""> /* Need this in addition to Stage3end_filter_concordant_tr, to</span>
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<a href="https://salsa.debian.org/med-team/gmap/-/compare/e36c478dd913ea44b8ccff832e1ed3c2409790ca...c42803c614bca47c818ce65af0a53b368a57e334#aeb285890115a453e6448fd7de6fc67bf8daf3a4"><strong>src/substring.c</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">rcsid</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"$Id: substring.c 2231<span class="idiff left right">62 2020-10-12 22:47:42</span>Z twu $"</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">rcsid</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"$Id: substring.c 2231<span class="idiff left right">73 2020-10-15 01:50:21</span>Z twu $"</span><span class="p">;</span></span>
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2
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifdef HAVE_CONFIG_H</span></span>
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <config.h></span></span>
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="5066" style="width: 35px; color: rgba(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="5066" style="width: 35px; color: rgba(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">@@ -5066,7 +5066,7 @@ Substring_count_mismatches_region (int *ref_nmismatches, T this, int trim_querys</td>
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5066
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5066
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<pre style="margin: 0;"> <span id="LC5066" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;"> assert(left_bound <= right_bound);</span></span>
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5067
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5067
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<pre style="margin: 0;"> <span id="LC5067" class="line" lang="c"><span class="c" style="color: #998; font-style: italic;">#endif</span></span>
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5068
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5068
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<pre style="margin: 0;"> <span id="LC5068" class="line" lang="c"></span>
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5069
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<pre style="margin: 0;">-<span id="LC5069" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">left_bound</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">right_bound</span><span class="p">)</span> <span class="p">{</span></span>
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5069
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<pre style="margin: 0;">+<span id="LC5069" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">left_bound</span> <span class="o" style="font-weight: 600;">><span class="idiff left right">=</span></span> <span class="n" style="color: #333;">right_bound</span><span class="p">)</span> <span class="p">{</span></span>
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5070
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5070
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<pre style="margin: 0;"> <span id="LC5070" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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5071
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5071
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<pre style="margin: 0;"> <span id="LC5071" class="line" lang="c"> <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;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">plusp</span><span class="p">)</span> <span class="p">{</span></span>
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5072
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5072
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<pre style="margin: 0;"> <span id="LC5072" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">Genome_count_mismatches_substring</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">ref_nmismatches</span><span class="p">),</span><span class="n" style="color: #333;">genomebits</span><span class="p">,</span><span class="n" style="color: #333;">genomebits_alt</span><span class="p">,</span><span class="n" style="color: #333;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">query_compress</span><span class="p">,</span><span class="n" style="color: #333;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">left</span><span class="p">,</span></span>
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