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<h3>
Nilesh Patra pushed to branch master
at <a href="https://salsa.debian.org/med-team/trnascan-se">Debian Med / trnascan-se</a>
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<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/trnascan-se/-/commit/cb78e14e4fcc857762256779d405b2ab83b5c41c">cb78e14e</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2021-05-12T00:48:11+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2.0.8+ds</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/trnascan-se/-/commit/a900f8b92d7a0ac2a1f7e90a055fea3790e0a7dc">a900f8b9</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2021-05-12T00:48:58+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/2.0.8+ds'
Update to upstream version '2.0.8+ds'
with Debian dir 1f15fefe27e6a9e19ded4113fc70731d632b52c0</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/trnascan-se/-/commit/009e9d891b21ee2cd35abe136b09fd6f88a1cac1">009e9d89</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2021-05-12T00:52:50+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Declare compliance with policy 4.5.1
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/trnascan-se/-/commit/9e93b054826b92e227c4e57a87e227512cf9abd9">9e93b054</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2021-05-12T00:53:17+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Interim changelog entry
</pre>
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<h4>14 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
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<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<li class="file-stats">
<a href="#9f08172398b69848ce5ead9edf12f5d8d19ade69">
src/dbmalloc.h
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<li class="file-stats">
<a href="#74e2d6b8ff46f06b6b9c65bb298c1e1015428472">
src/eufind_const.h
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<li class="file-stats">
<a href="#28ac8a248f2afb404fd34534d3adbf2a5411cce6">
src/eufind_main.c
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<li class="file-stats">
<a href="#2ec4de3977d59b159a56264a4cd3e50ecb6f5cd2">
src/gnuregex.c
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<li class="file-stats">
<a href="#1a70fd83e7798738ae855d6e2561819dc016cc07">
src/interleaved.c
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<li class="file-stats">
<a href="#6a5f197940ca1a2611c8d093444f9c38e2e37f24">
src/pavesi.c
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<li class="file-stats">
<a href="#824269a5f470ce9dbe294ed3ea010e149a3e30f3">
<span class="new-file">
+
src/pavesi.h
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<li class="file-stats">
<a href="#218a9b17519aab79ef0170ca8862fff3dc47b367">
src/scan_main.c
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<li class="file-stats">
<a href="#3d1bfef00fad70b7bf1d5205bc0e72a19e91d68e">
src/score_main.c
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<li class="file-stats">
<a href="#1470d52b08e57c87edc9967216f5758443ece714">
src/trnascan.c
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<li class="file-stats">
<a href="#25626e186d050c301ec3d731d261ed5fe0bf4d5e">
tRNAscan-SE.conf.src
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<li class="file-stats">
<a href="#10fd7c4f6f1e185010a4a71d1ef6b5fec8f9af8d">
tRNAscan-SE.src
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</ul>
<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/trnascan-se/-/compare/1b6189029a2b407f30b51676bb50702175420cd5...9e93b054826b92e227c4e57a87e227512cf9abd9#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">trnascan-se (2.0.8+ds-1) UNRELEASED; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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<td class="new_line diff-line-num new" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="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 2.0.8+ds</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> * Declare compliance with policy 4.5.1</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> -- Nilesh Patra <nilesh@debian.org> Wed, 12 May 2021 00:52:54 +0530</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">trnascan-se (2.0.7+ds-1) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> * New upstream version.</span>
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<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/trnascan-se/-/compare/1b6189029a2b407f30b51676bb50702175420cd5...9e93b054826b92e227c4e57a87e227512cf9abd9#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -7,7 +7,7 @@ Priority: optional</td>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">Build-Depends: debhelper-compat (= 13),</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> autoconf-archive,</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> infernal</span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext">Standards-Version: 4.5.<span class="idiff left right">0</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">Standards-Version: 4.5.<span class="idiff left right">1</span></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/trnascan-se</span>
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<td class="old_line diff-line-num" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/trnascan-se.git</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">Homepage: http://lowelab.ucsc.edu/tRNAscan-SE</span>
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<a href="https://salsa.debian.org/med-team/trnascan-se/-/compare/1b6189029a2b407f30b51676bb50702175420cd5...9e93b054826b92e227c4e57a87e227512cf9abd9#9f08172398b69848ce5ead9edf12f5d8d19ade69"><strong>src/dbmalloc.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;">/*</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * (c) Copyright 1990, 1991, 1992 Conor P. Cahill (uunet!virtech!cpcahil). </span></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * <span class="idiff left right">You may copy, distribute, and use this software as long as this</span></span></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * <span class="idiff left right">copyright statement is not removed</span>.</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * </span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * <span class="idiff left right">This code is distributed under GNU GENERAL PUBLIC LICENSE v3</span>.</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/*</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * $Id: malloc.h.org,v 1.31 1992/06/22 23:40:10 cpcahil Exp $</span></span>
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<a href="https://salsa.debian.org/med-team/trnascan-se/-/compare/1b6189029a2b407f30b51676bb50702175420cd5...9e93b054826b92e227c4e57a87e227512cf9abd9#74e2d6b8ff46f06b6b9c65bb298c1e1015428472"><strong>src/eufind_const.h</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifndef EUFIND_CONST_</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;">#define EUFIND_CONST_</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/* tRNA scanning cutoffs */</span></span>
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<pre style="margin: 0;"> <span id="LC5" 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">@@ -12,25 +14,25 @@</td>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define INT_SCORE_THRESH -31.25</span></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define TOT_SCORE_THRESH -31.8 </span><span class="cm" style="color: #998; font-style: italic;">/* -31.8 */</span></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define MAX_AB_BOX_DIST 140 </span><span class="cm" style="color: #998; font-style: italic;">/* not used anymore, instead</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define MAX_AB_BOX_DIST 140 </span><span class="cm" style="color: #998; font-style: italic;">/* not used anymore, instead<span class="idiff left right"> */</span></span></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* AB_BOX_DIST_RANGE used */</span></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define MIN_AB_BOX_DIST 24</span></span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define AB_BOX_DIST_RANGE 116 </span><span class="cm" style="color: #998; font-style: italic;">/* check this far over MIN_AB_BOX</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define AB_BOX_DIST_RANGE 116 </span><span class="cm" style="color: #998; font-style: italic;">/* check this far over MIN_AB_BOX<span class="idiff left right"> */</span></span></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* distance for A-B box pairs */</span></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define SEC_AB_BOX_DIST 26</span></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define SEC_BBOX_DIST_CORR 12</span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define MIN_BTERM_DIST 11</span></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define MAX_TERM_SEARCH 133 </span><span class="cm" style="color: #998; font-style: italic;">/* Max distance to search for termination</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define MAX_TERM_SEARCH 133 </span><span class="cm" style="color: #998; font-style: italic;">/* Max distance to search for termination<span class="idiff left right"> </span></span></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> signal (was 59, changed to 133 (as in</span></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> Pavesi paper) on 11/96</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> since was missing 4 yeast tRNAs */</span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define ABOX_LEN 21</span></span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define BBOX_LEN 11</span></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define MAX_OVLAP 10 </span><span class="cm" style="color: #998; font-style: italic;">/* max #bp tRNA hits are allowed to</span></span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> overlap */</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define MAX_OVLAP 10 </span><span class="cm" style="color: #998; font-style: italic;">/* max #bp tRNA hits are allowed to<span class="idiff left right"> </span></span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> <span class="idiff left right"> </span>overlap */</span></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="c"><span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">trna_info_s</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">iso_type</span><span class="p">[</span><span class="mi" style="color: #099;">5</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">@@ -45,7 +47,7 @@ struct trna_info_s {</td>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="c"><span class="k" style="font-weight: 600;">typedef</span> <span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">trna_info_s</span> <span class="n" style="color: #333;">TRNA_TYPE</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif </span><span class="cm" style="color: #998; font-style: italic;">/*EUFIND_CONST_*/</span></span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="c"></span></pre>
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<a href="https://salsa.debian.org/med-team/trnascan-se/-/compare/1b6189029a2b407f30b51676bb50702175420cd5...9e93b054826b92e227c4e57a87e227512cf9abd9#28ac8a248f2afb404fd34534d3adbf2a5411cce6"><strong>src/eufind_main.c</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -22,9 +22,11 @@</td>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <stdio.h></span></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <stdlib.h></span></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <string.h></span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <getopt.h></span></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "squid.h"</span></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "sqfuncs.h"</span></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "eufind_const.h"</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "pavesi.h"</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">eufind_version</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"1.1"</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">eufind_date</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"Aug 2000"</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">@@ -62,7 +64,7 @@ main (int argc, char **argv)</td>
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> not look for poly T terminator</span></span>
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> signal */</span></span>
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="c"> <span class="n" style="color: #333;">StrictMode</span><span class="p">,</span> <span class="cm" style="color: #998; font-style: italic;">/* require poly T terminator */</span></span>
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="c"> <span class="n" style="color: #333;">NoReformat</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/* flag to prevent extra work of </span></span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="c"> <span class="n" style="color: #333;">NoReformat</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/* flag to prevent extra work of <span class="idiff left right">*/</span></span></span>
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66
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68
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* changing seqs to DNA & upper case */</span></span>
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67
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69
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* alphabet */</span></span>
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68
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70
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="c"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="165" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="167" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -165,7 +167,7 @@ main (int argc, char **argv)</td>
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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;">Die</span><span class="p">(</span><span class="s" style="color: #d14;">"Memory failure, couldn't allocate sequence</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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166
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168
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<pre style="margin: 0;"> <span id="LC168" class="line" lang="c"> </span>
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167
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<td class="new_line diff-line-num" data-linenumber="169" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
169
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<pre style="margin: 0;"> <span id="LC169" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* integer-encode sequence */</span> </span>
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168
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<td class="new_line diff-line-num old" data-linenumber="170" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC168" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">errno</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">IntEncodeSeq</span><span class="p">(</span><span class="n" style="color: #333;">iseq</span><span class="p">,</span><span class="n" style="color: #333;">seq</span><span class="p">,</span><span class="n" style="color: #333;">sqinfo</span><span class="p">.</span><span class="n" style="color: #333;">len</span><span class="p">))</span></span>
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<td class="new_line diff-line-num new" data-linenumber="170" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p"><span class="idiff left">(</span>(</span><span class="n" style="color: #333;">errno</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">IntEncodeSeq</span><span class="p">(</span><span class="n" style="color: #333;">iseq</span><span class="p">,</span><span class="n" style="color: #333;">seq</span><span class="p">,</span><span class="n" style="color: #333;">sqinfo</span><span class="p">.</span><span class="n" style="color: #333;">len</span><span class="p">))<span class="idiff right">)</span></span></span>
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169
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<td class="new_line diff-line-num" data-linenumber="171" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
171
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<pre style="margin: 0;"> <span id="LC171" class="line" lang="c"> <span class="n" style="color: #333;">Die</span><span class="p">(</span><span class="s" style="color: #d14;">"Unable to encode sequence %s at base %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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170
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<td class="new_line diff-line-num" data-linenumber="172" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
172
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<pre style="margin: 0;"> <span id="LC172" class="line" lang="c"> <span class="n" style="color: #333;">sqinfo</span><span class="p">.</span><span class="n" style="color: #333;">name</span><span class="p">,</span><span class="n" style="color: #333;">errno</span><span class="p">);</span></span>
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171
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<td class="new_line diff-line-num" 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">
173
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<pre style="margin: 0;"> <span id="LC173" class="line" lang="c"> </span>
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<li id="2ec4de3977d59b159a56264a4cd3e50ecb6f5cd2">
<a href="https://salsa.debian.org/med-team/trnascan-se/-/compare/1b6189029a2b407f30b51676bb50702175420cd5...9e93b054826b92e227c4e57a87e227512cf9abd9#2ec4de3977d59b159a56264a4cd3e50ecb6f5cd2"><strong>src/gnuregex.c</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1611" style="width: 35px; color: rgba(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="1611" style="width: 35px; color: rgba(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">@@ -1611,10 +1611,12 @@ regex_compile (pattern, size, syntax, bufp)</td>
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1611
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1611
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<pre style="margin: 0;"> <span id="LC1611" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">syntax</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">RE_NO_BK_PARENS</span><span class="p">)</span> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">normal_backslash</span><span class="p">;</span></span>
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1612
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1612
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<pre style="margin: 0;"> <span id="LC1612" class="line" lang="c"></span>
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<td class="old_line diff-line-num" data-linenumber="1613" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1613
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<td class="new_line diff-line-num" data-linenumber="1613" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1613
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<pre style="margin: 0;"> <span id="LC1613" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">COMPILE_STACK_EMPTY</span><span class="p">)</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1614" style="width: 35px; color: rgba(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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1614
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<pre style="margin: 0;">+<span id="LC1614" class="line" lang="c"> <span class="p">{</span></span>
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1614
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<td class="new_line diff-line-num" data-linenumber="1615" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1615
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<pre style="margin: 0;"> <span id="LC1615" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">syntax</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">RE_UNMATCHED_RIGHT_PAREN_ORD</span><span class="p">)</span></span>
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1615
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<td class="new_line diff-line-num" data-linenumber="1616" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1616
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<pre style="margin: 0;"> <span id="LC1616" class="line" lang="c"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">normal_backslash</span><span class="p">;</span></span>
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1616
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<td class="new_line diff-line-num" data-linenumber="1617" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1617
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<pre style="margin: 0;"> <span id="LC1617" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span></span>
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1617
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<td class="new_line diff-line-num" data-linenumber="1618" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1618
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<pre style="margin: 0;"> <span id="LC1618" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">REG_ERPAREN</span><span class="p">;</span></span>
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1619
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<pre style="margin: 0;">+<span id="LC1619" class="line" lang="c"> <span class="p">}</span></span>
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1618
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1620
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<pre style="margin: 0;"> <span id="LC1620" class="line" lang="c"></span>
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1619
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1621
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<pre style="margin: 0;"> <span id="LC1621" class="line" lang="c"> <span class="nl">handle_close:</span></span>
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1620
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1622
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<pre style="margin: 0;"> <span id="LC1622" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">fixup_alt_jump</span><span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1633" style="width: 35px; color: rgba(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">@@ -1631,10 +1633,12 @@ regex_compile (pattern, size, syntax, bufp)</td>
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1631
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1633
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<pre style="margin: 0;"> <span id="LC1633" class="line" lang="c"></span>
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1632
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1634
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<pre style="margin: 0;"> <span id="LC1634" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* See similar code for backslashed left paren above. */</span></span>
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1633
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1635
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<pre style="margin: 0;"> <span id="LC1635" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">COMPILE_STACK_EMPTY</span><span class="p">)</span></span>
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1636
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<pre style="margin: 0;">+<span id="LC1636" class="line" lang="c"> <span class="p">{</span></span>
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1634
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1637
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<pre style="margin: 0;"> <span id="LC1637" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">syntax</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">RE_UNMATCHED_RIGHT_PAREN_ORD</span><span class="p">)</span></span>
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1635
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1638
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<pre style="margin: 0;"> <span id="LC1638" class="line" lang="c"> <span class="k" style="font-weight: 600;">goto</span> <span class="n" style="color: #333;">normal_char</span><span class="p">;</span></span>
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1636
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1639
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<pre style="margin: 0;"> <span id="LC1639" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span></span>
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1637
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1640
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<pre style="margin: 0;"> <span id="LC1640" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">REG_ERPAREN</span><span class="p">;</span></span>
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1641
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<pre style="margin: 0;">+<span id="LC1641" class="line" lang="c"> <span class="p">}</span></span>
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1642
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<pre style="margin: 0;"> <span id="LC1642" class="line" lang="c"></span>
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1639
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1643
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<pre style="margin: 0;"> <span id="LC1643" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Since we just checked for an empty stack above, this</span></span>
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1640
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1644
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<pre style="margin: 0;"> <span id="LC1644" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> ``can't happen''. */</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">@@ -2312,7 +2316,7 @@ typedef struct</td>
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2312
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2316
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<pre style="margin: 0;"> <span id="LC2316" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> value. Assumes the variable `fail_stack'. Probably should only</span></span>
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2313
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2317
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<pre style="margin: 0;"> <span id="LC2317" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> be called from within `PUSH_FAILURE_POINT'. */</span></span>
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2314
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2318
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<pre style="margin: 0;"> <span id="LC2318" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define PUSH_FAILURE_ITEM(item) \</span></span>
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<pre style="margin: 0;">-<span id="LC2315" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item</span></span>
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2319
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<pre style="margin: 0;">+<span id="LC2319" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) <span class="idiff left">((unsigned long) </span>item<span class="idiff right">)</span></span></span>
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2316
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2320
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<pre style="margin: 0;"> <span id="LC2320" class="line" lang="c"></span>
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2317
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2321
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<pre style="margin: 0;"> <span id="LC2321" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/* The complement operation. Assumes `fail_stack' is nonempty. */</span></span>
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2318
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2322
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<pre style="margin: 0;"> <span id="LC2322" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define POP_FAILURE_ITEM() fail_stack.stack[--fail_stack.avail]</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">@@ -2391,10 +2395,10 @@ typedef struct</td>
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2391
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2395
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<pre style="margin: 0;"> <span id="LC2395" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> } \</span></span>
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2392
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2396
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<pre style="margin: 0;"> <span id="LC2396" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> \</span></span>
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2393
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2397
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<pre style="margin: 0;"> <span id="LC2397" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> DEBUG_PRINT2 (" Pushing low active reg: %d\n", lowest_active_reg);\</span></span>
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2394
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<pre style="margin: 0;">-<span id="LC2394" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> PUSH_FAILURE_ITEM (<span class="idiff left right">(unsigned long)</span>lowest_active_reg); \</span></span>
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2398
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<pre style="margin: 0;">+<span id="LC2398" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> PUSH_FAILURE_ITEM (lowest_active_reg); <span class="idiff left right"> </span>\</span></span>
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2395
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2399
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<pre style="margin: 0;"> <span id="LC2399" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> \</span></span>
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2396
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2400
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<pre style="margin: 0;"> <span id="LC2400" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> DEBUG_PRINT2 (" Pushing high active reg: %d\n", highest_active_reg);\</span></span>
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2397
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<pre style="margin: 0;">-<span id="LC2397" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> PUSH_FAILURE_ITEM (<span class="idiff left right">(unsigned long)</span>highest_active_reg); \</span></span>
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2401
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<pre style="margin: 0;">+<span id="LC2401" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> PUSH_FAILURE_ITEM (highest_active_reg); \</span></span>
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2398
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2402
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<pre style="margin: 0;"> <span id="LC2402" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> \</span></span>
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2399
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2403
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<pre style="margin: 0;"> <span id="LC2403" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> DEBUG_PRINT2 (" Pushing pattern 0x%x: ", pattern_place); \</span></span>
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2400
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2404
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<pre style="margin: 0;"> <span id="LC2404" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> DEBUG_PRINT_COMPILED_PATTERN (bufp, pattern_place, pend); \</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2448" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2448,7 +2452,7 @@ typedef struct</td>
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2448
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2452
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<pre style="margin: 0;"> <span id="LC2452" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define POP_FAILURE_POINT(str, pat, low_reg, high_reg, regstart, regend, reg_info)\</span></span>
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2449
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2453
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<pre style="margin: 0;"> <span id="LC2453" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">{ \</span></span>
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2450
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2454
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<pre style="margin: 0;"> <span id="LC2454" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> DEBUG_STATEMENT (fail_stack_elt_t failure_id;) \</span></span>
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2451
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<pre style="margin: 0;">-<span id="LC2451" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> <span class="idiff left right">unsigned long</span> this_reg; \</span></span>
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2455
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<pre style="margin: 0;">+<span id="LC2455" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> <span class="idiff left right">int</span> this_reg; \</span></span>
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2452
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2456
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<pre style="margin: 0;"> <span id="LC2456" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> unsigned char *string_temp; \</span></span>
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2453
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2457
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<pre style="margin: 0;"> <span id="LC2457" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> \</span></span>
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2454
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2458
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<pre style="margin: 0;"> <span id="LC2458" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> assert (!FAIL_STACK_EMPTY ()); \</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2484" style="width: 35px; color: rgba(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">@@ -2480,14 +2484,14 @@ typedef struct</td>
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2480
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2484
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<pre style="margin: 0;"> <span id="LC2484" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> \</span></span>
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<pre style="margin: 0;"> <span id="LC2485" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> </span><span class="cm" style="color: #998; font-style: italic;">/* Restore register info. */</span><span class="cp" style="color: #999; font-weight: 600;"> \</span></span>
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<pre style="margin: 0;"> <span id="LC2486" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> high_reg = (unsigned long) POP_FAILURE_ITEM (); \</span></span>
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<pre style="margin: 0;">-<span id="LC2483" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> DEBUG_PRINT2 (" Popping high active reg: %<span class="idiff left right">u</span>\n", high_reg); \</span></span>
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<pre style="margin: 0;">+<span id="LC2487" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> DEBUG_PRINT2 (" Popping high active reg: %<span class="idiff left right">d</span>\n", high_reg); \</span></span>
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2488
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<pre style="margin: 0;"> <span id="LC2488" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> \</span></span>
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<pre style="margin: 0;"> <span id="LC2489" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> low_reg = (unsigned long) POP_FAILURE_ITEM (); \</span></span>
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<pre style="margin: 0;">-<span id="LC2486" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> DEBUG_PRINT2 (" Popping low active reg: %<span class="idiff left right">u</span>\n", low_reg); \</span></span>
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<pre style="margin: 0;">+<span id="LC2490" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> DEBUG_PRINT2 (" Popping low active reg: %<span class="idiff left right">d</span>\n", low_reg); \</span></span>
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2491
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<pre style="margin: 0;"> <span id="LC2491" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> \</span></span>
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2492
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<pre style="margin: 0;"> <span id="LC2492" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> for (this_reg = high_reg; this_reg >= low_reg; this_reg--) \</span></span>
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<pre style="margin: 0;"> <span id="LC2493" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> { \</span></span>
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<pre style="margin: 0;">-<span id="LC2490" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> DEBUG_PRINT2 (" Popping reg: %<span class="idiff left right">u</span>\n", this_reg); \</span></span>
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<pre style="margin: 0;">+<span id="LC2494" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> DEBUG_PRINT2 (" Popping reg: %<span class="idiff left right">d</span>\n", this_reg); \</span></span>
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<pre style="margin: 0;"> <span id="LC2495" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> \</span></span>
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<pre style="margin: 0;"> <span id="LC2496" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> reg_info[this_reg].word = POP_FAILURE_ITEM (); \</span></span>
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<pre style="margin: 0;"> <span id="LC2497" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"> DEBUG_PRINT2 (" info: 0x%x\n", reg_info[this_reg]); \</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2818" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2818,7 +2822,7 @@ re_set_registers (bufp, regs, num_regs, starts, ends)</td>
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2822
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<pre style="margin: 0;"> <span id="LC2822" class="line" lang="c"> <span class="p">{</span></span>
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2819
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2823
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<pre style="margin: 0;"> <span id="LC2823" class="line" lang="c"> <span class="n" style="color: #333;">bufp</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">regs_allocated</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">REGS_UNALLOCATED</span><span class="p">;</span></span>
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2824
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<pre style="margin: 0;"> <span id="LC2824" class="line" lang="c"> <span class="n" style="color: #333;">regs</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">num_regs</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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2821
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<pre style="margin: 0;">-<span id="LC2821" class="line" lang="c"> <span class="n" style="color: #333;">regs</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">regs</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">regoff_t</span><span class="p">)</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC2825" class="line" lang="c"> <span class="n" style="color: #333;">regs</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">regs</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">regoff_t</span><span class="o" style="font-weight: 600;"><span class="idiff left right">*</span></span><span class="p">)</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC2826" class="line" lang="c"> <span class="p">}</span></span>
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2823
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2827
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<pre style="margin: 0;"> <span id="LC2827" class="line" lang="c"><span class="p">}</span></span>
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2824
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2828
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<pre style="margin: 0;"> <span id="LC2828" class="line" lang="c"><span class="err" style="color: #a61717; background-color: #e3d2d2;"></span></span>
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<a href="https://salsa.debian.org/med-team/trnascan-se/-/compare/1b6189029a2b407f30b51676bb50702175420cd5...9e93b054826b92e227c4e57a87e227512cf9abd9#1a70fd83e7798738ae855d6e2561819dc016cc07"><strong>src/interleaved.c</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="143" style="width: 35px; color: rgba(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="143" style="width: 35px; color: rgba(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">@@ -143,7 +143,7 @@ dataline_clustal(char *buf, char *expected_name)</td>
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143
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143
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<pre style="margin: 0;"> <span id="LC143" class="line" lang="c"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">buf</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">isspace</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">buf</span><span class="p">))</span> <span class="n" style="color: #333;">buf</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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144
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144
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<pre style="margin: 0;"> <span id="LC144" class="line" lang="c"> <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;">buf</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'\0'</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">strchr</span><span class="p">(</span><span class="n" style="color: #333;">commentsyms</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">buf</span><span class="p">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">)</span> </span>
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145
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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;">return</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/* blank or comment */</span></span>
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<td class="old_line diff-line-num old" data-linenumber="146" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
146
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<td class="new_line diff-line-num old" data-linenumber="146" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC146" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">expected_name</span> <span class="o" style="font-weight: 600;">!=</span> <span class="nb" style="color: #0086b3;">NULL</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">strncmp</span><span class="p">(</span><span class="n" style="color: #333;">buf</span><span class="p">,</span> <span class="n" style="color: #333;">expected_name</span><span class="p">,</span> <span class="n" style="color: #333;">strlen</span><span class="p">(</span><span class="n" style="color: #333;">expected_name</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 class="idiff left right">)</span></span></span>
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<td class="old_line diff-line-num new" data-linenumber="147" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="146" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">expected_name</span> <span class="o" style="font-weight: 600;">!=</span> <span class="nb" style="color: #0086b3;">NULL</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">strncmp</span><span class="p">(</span><span class="n" style="color: #333;">buf</span><span class="p">,</span> <span class="n" style="color: #333;">expected_name</span><span class="p">,</span> <span class="n" style="color: #333;">strlen</span><span class="p">(</span><span class="n" style="color: #333;">expected_name</span><span class="p">)<span class="idiff left right">)</span></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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147
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<td class="new_line diff-line-num" data-linenumber="147" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
147
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<pre style="margin: 0;"> <span id="LC147" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/* matches expected seq name */</span></span>
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<td class="old_line diff-line-num" data-linenumber="148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
148
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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;">for</span> <span class="p">(;</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">buf</span> <span class="o" style="font-weight: 600;">!=</span> <span class="sc" style="color: #d14;">'\0'</span><span class="p">;</span> <span class="n" style="color: #333;">buf</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>
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<td class="old_line diff-line-num" data-linenumber="149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
149
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149
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<pre style="margin: 0;"> <span id="LC149" class="line" lang="c"> <span class="p">{</span> <span class="cm" style="color: #998; font-style: italic;">/* Clustal has no coord lines to worry about */</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="213" style="width: 35px; color: rgba(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="213" style="width: 35px; color: rgba(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">@@ -213,7 +213,7 @@ dataline_MSF(char *buf, char *expected_name)</td>
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213
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213
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<pre style="margin: 0;"> <span id="LC213" class="line" lang="c"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">buf</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">isspace</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">buf</span><span class="p">))</span> <span class="n" style="color: #333;">buf</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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214
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214
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<pre style="margin: 0;"> <span id="LC214" class="line" lang="c"> <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;">buf</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'\0'</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">strchr</span><span class="p">(</span><span class="n" style="color: #333;">commentsyms</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">buf</span><span class="p">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">)</span> </span>
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215
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215
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<pre style="margin: 0;"> <span id="LC215" 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 class="cm" style="color: #998; font-style: italic;">/* blank or comment */</span></span>
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216
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<pre style="margin: 0;">-<span id="LC216" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">expected_name</span> <span class="o" style="font-weight: 600;">!=</span> <span class="nb" style="color: #0086b3;">NULL</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">strncmp</span><span class="p">(</span><span class="n" style="color: #333;">buf</span><span class="p">,</span> <span class="n" style="color: #333;">expected_name</span><span class="p">,</span> <span class="n" style="color: #333;">strlen</span><span class="p">(</span><span class="n" style="color: #333;">expected_name</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 class="idiff left right">)</span></span></span>
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<td class="old_line diff-line-num new" data-linenumber="217" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="216" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
216
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">expected_name</span> <span class="o" style="font-weight: 600;">!=</span> <span class="nb" style="color: #0086b3;">NULL</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">strncmp</span><span class="p">(</span><span class="n" style="color: #333;">buf</span><span class="p">,</span> <span class="n" style="color: #333;">expected_name</span><span class="p">,</span> <span class="n" style="color: #333;">strlen</span><span class="p">(</span><span class="n" style="color: #333;">expected_name</span><span class="p">)<span class="idiff left right">)</span></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="old_line diff-line-num" data-linenumber="217" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
217
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<td class="new_line diff-line-num" data-linenumber="217" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
217
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<pre style="margin: 0;"> <span id="LC217" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/* matches expected seq name */</span></span>
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<pre style="margin: 0;"> <span id="LC218" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(;</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">buf</span> <span class="o" style="font-weight: 600;">!=</span> <span class="sc" style="color: #d14;">'\0'</span><span class="p">;</span> <span class="n" style="color: #333;">buf</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC219" class="line" lang="c"> <span class="p">{</span> <span class="cm" style="color: #998; font-style: italic;">/* MSF has coordinate lines to worry about */</span></span>
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<a href="https://salsa.debian.org/med-team/trnascan-se/-/compare/1b6189029a2b407f30b51676bb50702175420cd5...9e93b054826b92e227c4e57a87e227512cf9abd9#6a5f197940ca1a2611c8d093444f9c38e2e37f24"><strong>src/pavesi.c</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -24,6 +24,7 @@</td>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <string.h></span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "squid.h"</span></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "eufind_const.h"</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "pavesi.h"</span></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/* #define NO_AMBIG -use this option to eliminate conservative</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * calling of 'N's as best possible matches</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">@@ -88,7 +89,7 @@ float BTermDistSc_Mat[BTERM_MAT_SIZE] = {-0.54,-1.40,-2.80,-3.36,</td>
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<pre style="margin: 0;"> <span id="LC89" class="line" lang="c"> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">3</span><span class="p">.</span><span class="mi" style="color: #099;">24</span><span class="p">,</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">5</span><span class="p">.</span><span class="mi" style="color: #099;">44</span><span class="p">,</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">5</span><span class="p">.</span><span class="mi" style="color: #099;">44</span><span class="p">,</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">4</span><span class="p">.</span><span class="mo" style="color: #099;">06</span><span class="p">,</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">5</span><span class="p">.</span><span class="mi" style="color: #099;">44</span><span class="p">};</span> </span>
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC91" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right">int</span></span></span>
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right">void</span></span></span>
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<pre style="margin: 0;"> <span id="LC93" class="line" lang="c"><span class="nf" style="color: #900; font-weight: 600;">Init_tRNA</span><span class="p">(</span><span class="n" style="color: #333;">TRNA_TYPE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">tRNA</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC94" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC95" class="line" lang="c"> <span class="n" style="color: #333;">strcpy</span><span class="p">(</span><span class="n" style="color: #333;">tRNA</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">iso_type</span><span class="p">,</span><span class="s" style="color: #d14;">"???"</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="135" style="width: 35px; color: rgba(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="136" style="width: 35px; color: rgba(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">@@ -135,15 +136,14 @@ GetBbox (float *score, int *seqidx, char *iseq, int seqlen,</td>
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<pre style="margin: 0;"> <span id="LC136" class="line" lang="c"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">Bbox_Mat</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;">iseq</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;">j</span><span class="p">])][</span><span class="n" style="color: #333;">j</span><span class="p">];</span></span>
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<pre style="margin: 0;"> <span id="LC137" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC138" class="line" lang="c"> <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;">score</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">BBOX_CUTOFF</span><span class="p">)</span> <span class="p">{</span></span>
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138
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<pre style="margin: 0;">-<span id="LC138" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">verbose</span><span class="p">)</span></span>
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139
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<pre style="margin: 0;">-<span id="LC139" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">strand</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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140
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<pre style="margin: 0;">-<span id="LC140" class="line" lang="c"> <span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"Bbox at %i (End=%d), Sc= %.2f</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;">i</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;">BBOX_LEN</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">11</span><span class="p">,</span></span>
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141
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<pre style="margin: 0;">-<span id="LC141" class="line" lang="c"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">score</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC142" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC143" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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144
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<pre style="margin: 0;">-<span id="LC144" class="line" lang="c"> <span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"Bbox at %i (End=%d), Sc= %.2f</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;">seqlen</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="mi" style="color: #099;">1</span><span class="p">,</span></span>
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145
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<pre style="margin: 0;">-<span id="LC145" class="line" lang="c"> <span class="n" style="color: #333;">seqlen</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="n" style="color: #333;">BBOX_LEN</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">11</span><span class="p">)</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">,</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">score</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC146" class="line" lang="c"> <span class="p">}</span></span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">verbose</span><span class="p">)</span> <span class="p">{</span></span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">strand</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="c"> <span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"Bbox at %i (End=%d), Sc= %.2f</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;">i</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;">BBOX_LEN</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">11</span><span class="p">,</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">score</span><span class="p">);</span></span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="c"> <span class="p">}</span></span>
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143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="c"> <span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"Bbox at %i (End=%d), Sc= %.2f</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;">seqlen</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="mi" style="color: #099;">1</span><span class="p">,</span><span class="n" style="color: #333;">seqlen</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="n" style="color: #333;">BBOX_LEN</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">11</span><span class="p">)</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">,</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">score</span><span class="p">);</span></span>
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145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="c"> <span class="p">}</span></span>
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146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC147" class="line" lang="c"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">seqidx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</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;">return</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC149" class="line" lang="c"> <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">@@ -221,7 +221,7 @@ GetSecABox(TRNA_TYPE *tRNA, char *seq)</td>
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<pre style="margin: 0;"> <span id="LC221" class="line" lang="c"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC222" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC223" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC224" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right">int</span></span></span>
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left right">void</span></span></span>
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<pre style="margin: 0;"> <span id="LC225" class="line" lang="c"><span class="nf" style="color: #900; font-weight: 600;">GetBestABox</span> <span class="p">(</span><span class="n" style="color: #333;">TRNA_TYPE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">tRNA</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">iseq</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">seqlen</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC226" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">strand</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">verbose</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">Max_AB_dist</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">prev_Abox_st</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC227" class="line" lang="c"><span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="257" style="width: 35px; color: rgba(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">@@ -257,7 +257,7 @@ GetBestABox (TRNA_TYPE *tRNA, char *seq, char *iseq, int seqlen,</td>
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257
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<pre style="margin: 0;"> <span id="LC257" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* score gap at pos 17 by looking for conserved 'GG' at pos 18 &</span></span>
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<pre style="margin: 0;"> <span id="LC258" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> 19 */</span></span>
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<pre style="margin: 0;"> <span id="LC259" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC260" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p"><span class="idiff left">(</span>(</span><span class="n" style="color: #333;">seq</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;">j</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'G'</span><span class="p">)<span class="idiff right">)</span></span> <span class="p">{</span> <span class="cm" style="color: #998; font-style: italic;">/* && (seq[i+j+1] == 'G')) { */</span></span>
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<pre style="margin: 0;">+<span id="LC260" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">seq</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;">j</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'G'</span><span class="p">)</span> <span class="p">{</span> <span class="cm" style="color: #998; font-style: italic;">/* && (seq[i+j+1] == 'G')) { */</span></span>
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261
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<pre style="margin: 0;"> <span id="LC261" class="line" lang="c"> <span class="n" style="color: #333;">sc2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Abox_Mat</span><span class="p">[</span><span class="n" style="color: #333;">GAP_ROW</span><span class="p">][</span><span class="n" style="color: #333;">j</span><span class="p">];</span></span>
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<pre style="margin: 0;"> <span id="LC262" class="line" lang="c"> <span class="n" style="color: #333;">offset1</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC263" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="317" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -317,7 +317,7 @@ GetBestABox (TRNA_TYPE *tRNA, char *seq, char *iseq, int seqlen,</td>
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317
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<pre style="margin: 0;"> <span id="LC317" class="line" lang="c"> <span class="n" style="color: #333;">tRNA</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">AboxSc</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sc1</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">sc2</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">sc3</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC318" class="line" lang="c"> <span class="n" style="color: #333;">best_offset1</span><span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">offset1</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC319" class="line" lang="c"> <span class="n" style="color: #333;">best_gap</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gapct</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC320" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">verbose</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC320" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">verbose</span><span class="p">)</span><span class="idiff left"> </span><span class="p"><span class="idiff right">{</span></span></span>
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321
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<pre style="margin: 0;"> <span id="LC321" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">strand</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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322
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<pre style="margin: 0;"> <span id="LC322" class="line" lang="c"> <span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"Abox at %d (St=%d) A:%.2f AB(%d):%.2f I:%.2f</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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323
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<pre style="margin: 0;"> <span id="LC323" class="line" lang="c"> <span class="n" style="color: #333;">i</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;">5</span><span class="p">,</span><span class="n" style="color: #333;">tRNA</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">AboxSc</span><span class="p">,</span> <span class="n" style="color: #333;">tRNA</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Bbox_st</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">abox_end</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span><span class="n" style="color: #333;">tRNA</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">ABdistSc</span><span class="p">,</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="329" style="width: 35px; color: rgba(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">@@ -329,7 +329,7 @@ GetBestABox (TRNA_TYPE *tRNA, char *seq, char *iseq, int seqlen,</td>
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<pre style="margin: 0;"> <span id="LC329" class="line" lang="c"> <span class="n" style="color: #333;">tRNA</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">Bbox_st</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">abox_end</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span><span class="n" style="color: #333;">tRNA</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">ABdistSc</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC330" class="line" lang="c"> <span class="n" style="color: #333;">tRNA</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">AboxSc</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">tRNA</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">BboxSc</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">tRNA</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">ABdistSc</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC331" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC332" class="line" lang="c"><span class="idiff left"> </span> <span class="idiff right"> </span></span>
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<pre style="margin: 0;">+<span id="LC332" class="line" lang="c"> <span class="p"><span class="idiff left right">}</span></span></span>
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<pre style="margin: 0;"> <span id="LC333" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC334" class="line" lang="c"> <span class="p">}</span> <span class="cm" style="color: #998; font-style: italic;">/* for gapct, enumerating all possible gaps */</span></span>
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<pre style="margin: 0;"> <span id="LC335" class="line" lang="c"> <span class="p">}</span> <span class="cm" style="color: #998; font-style: italic;">/* for i, starting pos for A box */</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="373" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -373,6 +373,7 @@ GetBestTrxTerm (TRNA_TYPE *tRNA, char *seq, int seqlen,</td>
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373
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<pre style="margin: 0;"> <span id="LC373" class="line" lang="c"> <span class="n" style="color: #333;">tRNA</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">TermSc</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">MAX_PENALTY</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC374" 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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<pre style="margin: 0;"> <span id="LC375" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC376" 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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<pre style="margin: 0;"> <span id="LC377" class="line" lang="c"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC378" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC379" class="line" lang="c"></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;">/* eufindtRNA - Eukaryotic tRNA finder</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * pavesi.h - functions for finding transcriptional control regions </span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * C implementation of algorithm described by Pavesi, Conterio, </span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * Bolchi, Dieci, & Ottonello in NAR 22:1247-56 (94)</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * "Identification of new eukaryotic tRNA genes in genomic DNA</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * databases by a multistep weight matix analysis of transcriptional</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * control regions"</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * To be used in tRNAscan-SE package to increase sensitivity by</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * complementing tRNAscan 1.3 first-pass scan</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * by Todd MJ Lowe 4/8/96</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * Uses Sean Eddy's function library for biological sequence analysis</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * (Squid v1.5g)</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "squid.h"</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "eufind_const.h"</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">Init_tRNA</span><span class="p">(</span><span class="n" style="color: #333;">TRNA_TYPE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">tRNA</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">IntEncodeSeq</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;">intseq</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">seqlen</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">GetBbox</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">score</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;">seqidx</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;">iseq</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">seqlen</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">strand</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">verbose</span><span class="p">);</span></span>
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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="kt" style="color: #458; font-weight: 600;">float</span> <span class="nf" style="color: #900; font-weight: 600;">Get_ABdist_weight</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ABdist</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">GetSecABox</span><span class="p">(</span><span class="n" style="color: #333;">TRNA_TYPE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">tRNA</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">seq</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">GetBestABox</span> <span class="p">(</span><span class="n" style="color: #333;">TRNA_TYPE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">tRNA</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">iseq</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">seqlen</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">strand</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">verbose</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">Max_AB_dist</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">prev_Abox_st</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">GetBestTrxTerm</span> <span class="p">(</span><span class="n" style="color: #333;">TRNA_TYPE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">tRNA</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">seqlen</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">TermPenalty</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">Get_IsoType</span> <span class="p">(</span><span class="n" style="color: #333;">TRNA_TYPE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">tRNA</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">Get_anticodon</span> <span class="p">(</span><span class="n" style="color: #333;">TRNA_TYPE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">tRNA</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">seq</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">Get_tRNA_stats</span> <span class="p">(</span><span class="n" style="color: #333;">TRNA_TYPE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">tRNA</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">seqlen</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">strand</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">Save_tRNA</span> <span class="p">(</span><span class="n" style="color: #333;">TRNA_TYPE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">tRNA</span><span class="p">,</span> <span class="n" style="color: #333;">SQINFO</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">sqinfo</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">strand</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ShowScores</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">sqoffset</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">tRNAOverlap</span> <span class="p">(</span><span class="n" style="color: #333;">TRNA_TYPE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">tRNA1</span><span class="p">,</span> <span class="n" style="color: #333;">TRNA_TYPE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">tRNA2</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">strand</span><span class="p">);</span></span></pre>
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<a href="https://salsa.debian.org/med-team/trnascan-se/-/compare/1b6189029a2b407f30b51676bb50702175420cd5...9e93b054826b92e227c4e57a87e227512cf9abd9#218a9b17519aab79ef0170ca8862fff3dc47b367"><strong>src/scan_main.c</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -9,10 +9,11 @@</td>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <string.h></span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <time.h></span></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <math.h></span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <getopt.h></span></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifdef NEED_GETOPTH</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"><span class="idiff left right">/*</span>#ifdef NEED_GETOPTH</span></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">#include <getopt.h></span></span>
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<pre style="margin: 0;">-<span id="LC15" 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="LC16" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">#endif<span class="idiff left right">*/</span></span></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "structs.h"</span></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "funcs.h"</span></span>
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<a href="https://salsa.debian.org/med-team/trnascan-se/-/compare/1b6189029a2b407f30b51676bb50702175420cd5...9e93b054826b92e227c4e57a87e227512cf9abd9#3d1bfef00fad70b7bf1d5205bc0e72a19e91d68e"><strong>src/score_main.c</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -11,10 +11,11 @@</td>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <string.h></span></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <time.h></span></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <math.h></span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <getopt.h></span></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifdef NEED_GETOPTH</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"><span class="idiff left right">/*</span>#ifdef NEED_GETOPTH</span></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">#include <getopt.h></span></span>
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<pre style="margin: 0;">-<span id="LC17" 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="LC18" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">#endif<span class="idiff left right">*/</span></span></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "structs.h"</span></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "funcs.h"</span></span>
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<a href="https://salsa.debian.org/med-team/trnascan-se/-/compare/1b6189029a2b407f30b51676bb50702175420cd5...9e93b054826b92e227c4e57a87e227512cf9abd9#1470d52b08e57c87edc9967216f5758443ece714"><strong>src/trnascan.c</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -69,6 +69,7 @@ where supported options are:\n\</td>
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <stdio.h></span></span>
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <stdlib.h></span></span>
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <ctype.h></span></span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <getopt.h></span></span>
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifdef MEMDEBUG</span></span>
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "dbmalloc.h"</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">@@ -332,7 +333,7 @@ printresult(FILE *fpo, /* output file pointer */</td>
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<pre style="margin: 0;"> <span id="LC333" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">sqoffset</span> <span class="cm" style="color: #998; font-style: italic;">/* offset nucleotide numbering by this much (set with -i param) */</span></span>
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<pre style="margin: 0;"> <span id="LC334" class="line" lang="c"> <span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC335" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC335" class="line" lang="c"><span class="n" style="color: #333;">main</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">argc</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">argv</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC336" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">int</span></span><span class="idiff right"> </span><span class="nf" style="color: #900; font-weight: 600;">main</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">argc</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">argv</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC337" class="line" lang="c"><span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC338" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* pointers to the different files fpi=input file, fpo=output file, </span></span>
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339
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<pre style="margin: 0;"> <span id="LC339" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> fpcons1= T-Psi-C matrix file, fpcons2= D matrix file */</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1177" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1176,8 +1177,8 @@ for (i=0; i<*lsig; i++)</td>
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1176
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1177
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<pre style="margin: 0;"> <span id="LC1177" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">table_cons</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">][</span><span class="n" style="color: #333;">j</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="mi" style="color: #099;">0</span><span class="p">)</span></span>
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1177
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1178
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<pre style="margin: 0;"> <span id="LC1178" class="line" lang="c"> <span class="p">{</span></span>
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1178
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1179
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<pre style="margin: 0;"> <span id="LC1179" class="line" lang="c"> <span class="n" style="color: #333;">k</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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1179
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<pre style="margin: 0;">-<span id="LC1179" class="line" lang="c"> <span class="n" style="color: #333;">table_inv</span><span class="p">[</span><span class="n" style="color: #333;">k</span><span class="p">][</span><span class="mi" style="color: #099;"><span class="idiff left right">1</span></span><span class="p">]</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">i</span><span class="p">;</span></span>
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1180
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<pre style="margin: 0;">-<span id="LC1180" class="line" lang="c"> <span class="n" style="color: #333;">table_inv</span><span class="p">[</span><span class="n" style="color: #333;">k</span><span class="p">][</span><span class="mi" style="color: #099;"><span class="idiff left right">2</span></span><span class="p">]</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">j</span><span class="p">;</span></span>
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1180
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<pre style="margin: 0;">+<span id="LC1180" class="line" lang="c"> <span class="n" style="color: #333;">table_inv</span><span class="p">[</span><span class="n" style="color: #333;">k</span><span class="p">][</span><span class="mi" style="color: #099;"><span class="idiff left right">0</span></span><span class="p">]</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">i</span><span class="p">;</span></span>
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1181
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<pre style="margin: 0;">+<span id="LC1181" class="line" lang="c"> <span class="n" style="color: #333;">table_inv</span><span class="p">[</span><span class="n" style="color: #333;">k</span><span class="p">][</span><span class="mi" style="color: #099;"><span class="idiff left right">1</span></span><span class="p">]</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">j</span><span class="p">;</span></span>
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1181
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1182
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<pre style="margin: 0;"> <span id="LC1182" class="line" lang="c"> <span class="p">}</span></span>
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1182
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1183
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<pre style="margin: 0;"> <span id="LC1183" class="line" lang="c"> <span class="p">}</span></span>
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1184
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<pre style="margin: 0;"> <span id="LC1184" class="line" lang="c"> <span class="p">}</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1418" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1419" style="width: 35px; color: rgba(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">@@ -1418,7 +1419,7 @@ return seqlen;</td>
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1418
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1419
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<pre style="margin: 0;"> <span id="LC1419" class="line" lang="c"></span>
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1419
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1420
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<pre style="margin: 0;"> <span id="LC1420" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/* Calls to this function eliminated for efficiency T. Lowe 11/95 */</span></span>
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1420
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1421
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<pre style="margin: 0;"> <span id="LC1421" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC1421" class="line" lang="c"><span class="n" style="color: #333;">myindex</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;">s</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;">t</span><span class="p">)</span></span>
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1422
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<pre style="margin: 0;">+<span id="LC1422" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">int</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">myindex</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;">s</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;">t</span><span class="p">)</span></span>
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1422
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1423
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<pre style="margin: 0;"> <span id="LC1423" class="line" lang="c"><span class="p">{</span></span>
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1423
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1424
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<pre style="margin: 0;"> <span id="LC1424" 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 class="n" style="color: #333;">j</span><span class="p">,</span> <span class="n" style="color: #333;">k</span><span class="p">;</span></span>
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1424
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1425
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<pre style="margin: 0;"> <span id="LC1425" 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;">s</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="sc" style="color: #d14;">'\0'</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1477" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1476,10 +1477,10 @@ int readsignal(char *ptr, /* pointer to the sequence */</td>
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1476
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1477
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<pre style="margin: 0;"> <span id="LC1477" class="line" lang="c"> </span>
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1477
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1478
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<pre style="margin: 0;"> <span id="LC1478" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/* (original code commented out)</span></span>
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1478
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1479
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<pre style="margin: 0;"> <span id="LC1479" class="line" lang="c"></span>
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1479
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<pre style="margin: 0;">-<span id="LC1479" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> temp[0]= *(ptr+table_inv[k][<span class="idiff left right">1</span>]);</span></span>
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1480
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<pre style="margin: 0;">+<span id="LC1480" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> temp[0]= *(ptr+table_inv[k][<span class="idiff left right">0</span>]);</span></span>
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1480
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1481
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<pre style="margin: 0;"> <span id="LC1481" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> j = myindex(base,temp); */</span></span>
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1481
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1482
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<pre style="margin: 0;"> <span id="LC1482" class="line" lang="c"> </span>
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1482
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<pre style="margin: 0;">-<span id="LC1482" class="line" lang="c"> <span class="k" style="font-weight: 600;">switch</span> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">ptr</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">table_inv</span><span class="p">[</span><span class="n" style="color: #333;">k</span><span class="p">][</span><span class="mi" style="color: #099;"><span class="idiff left right">1</span></span><span class="p">]))</span> <span class="p">{</span></span>
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1483
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<pre style="margin: 0;">+<span id="LC1483" class="line" lang="c"> <span class="k" style="font-weight: 600;">switch</span> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">ptr</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">table_inv</span><span class="p">[</span><span class="n" style="color: #333;">k</span><span class="p">][</span><span class="mi" style="color: #099;"><span class="idiff left right">0</span></span><span class="p">]))</span> <span class="p">{</span></span>
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1483
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1484
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<pre style="margin: 0;"> <span id="LC1484" class="line" lang="c"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'a'</span><span class="p">:</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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1484
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1485
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<pre style="margin: 0;"> <span id="LC1485" class="line" lang="c"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'c'</span><span class="p">:</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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1485
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1486
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<pre style="margin: 0;"> <span id="LC1486" class="line" lang="c"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'g'</span><span class="p">:</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">2</span><span class="p">;</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1491" style="width: 35px; color: rgba(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="1492" style="width: 35px; color: rgba(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">@@ -1491,9 +1492,9 @@ int readsignal(char *ptr, /* pointer to the sequence */</td>
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1491
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1492
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<pre style="margin: 0;"> <span id="LC1492" class="line" lang="c"></span>
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1492
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1493
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<pre style="margin: 0;"> <span id="LC1493" class="line" lang="c"></span>
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1493
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1494
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<pre style="margin: 0;"> <span id="LC1494" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifdef NO_AMBIG</span></span>
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1494
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<pre style="margin: 0;">-<span id="LC1494" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">table_inv</span><span class="p">[</span><span class="n" style="color: #333;">k</span><span class="p">][</span><span class="mi" style="color: #099;"><span class="idiff left right">2</span></span><span class="p">])</span> </span>
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1495
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<pre style="margin: 0;">+<span id="LC1495" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">table_inv</span><span class="p">[</span><span class="n" style="color: #333;">k</span><span class="p">][</span><span class="mi" style="color: #099;"><span class="idiff left right">1</span></span><span class="p">])</span> </span>
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1495
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1496
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<pre style="margin: 0;"> <span id="LC1496" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#else</span></span>
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1496
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<pre style="margin: 0;">-<span id="LC1496" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">table_inv</span><span class="p">[</span><span class="n" style="color: #333;">k</span><span class="p">][</span><span class="mi" style="color: #099;"><span class="idiff left right">2</span></span><span class="p">])</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">==</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">))</span> </span>
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<pre style="margin: 0;">+<span id="LC1497" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">table_inv</span><span class="p">[</span><span class="n" style="color: #333;">k</span><span class="p">][</span><span class="mi" style="color: #099;"><span class="idiff left right">1</span></span><span class="p">])</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">==</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">))</span> </span>
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<pre style="margin: 0;"> <span id="LC1498" 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="LC1499" class="line" lang="c"> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">ninv</span><span class="p">)</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC1500" 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">@@ -29,6 +29,8 @@ organelle_cm_cutoff: 15</td>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="plaintext">isotype_cm_cutoff.euk: 20</span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="plaintext">isotype_cm_cutoff.arch: 20</span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="plaintext">isotype_cm_cutoff.bact: 20</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">isotype_cm_cutoff.mito_mammal: 20</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">isotype_cm_cutoff.mito_vert: 20</span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="plaintext"># max size of -w parameter passed to covels when using a pre-scanner (eufind or tRNAscan)</span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="plaintext">max_tRNA_length: 500</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"># tRNAscan-SE: a program for improved detection of transfer RNA</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"># genes in genomic sequence</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">#</span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext"># Version 2.0.<span class="idiff left right">7</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"># Version 2.0.<span class="idiff left right">8</span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">#</span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext"># Copyright (C) 202<span class="idiff left right">0</span> Patricia Chan and Todd Lowe </span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"># Copyright (C) 202<span class="idiff left right">1</span> Patricia Chan and Todd Lowe </span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">#</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"># School of Engineering, University of California, Santa Cruz</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"># trna@soe.ucsc.edu</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -39,8 +39,8 @@ use tRNAscanSE::IntResultFile;</td>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="plaintext">use tRNAscanSE::MultiResultFile;</span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="plaintext">use tRNAscanSE::SS;</span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="plaintext">our $version = "2.0.<span class="idiff left right">7</span>"; </span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="plaintext">our $release_date = "<span class="idiff left">Oct</span> 202<span class="idiff right">0</span>";</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext">our $version = "2.0.<span class="idiff left right">8</span>"; </span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext">our $release_date = "<span class="idiff left">May</span> 202<span class="idiff right">1</span>";</span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="plaintext">our $program_id = "tRNAscan-SE-".$version;</span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="plaintext"># modified by 'make'</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="594" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -594,7 +594,8 @@ sub prepare_intron_scan</td>
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594
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<pre style="margin: 0;"> <span id="LC594" class="line" lang="plaintext"># clean up temp files</span>
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595
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<pre style="margin: 0;"> <span id="LC595" class="line" lang="plaintext">sub cleanup</span>
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<pre style="margin: 0;"> <span id="LC596" class="line" lang="plaintext">{ </span>
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<pre style="margin: 0;">-<span id="LC597" class="line" lang="plaintext"> system("rm -f ".$global_constants->get("temp_dir")."/tscan$$".'*');</span>
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<pre style="margin: 0;">+<span id="LC597" class="line" lang="plaintext"> system("rm -f ".$global_constants->get("temp_dir")."/tscan$$"."_*");</span>
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<pre style="margin: 0;">+<span id="LC598" class="line" lang="plaintext"> system("rm -f ".$global_constants->get("temp_dir")."/tscan$$".".*");</span>
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<pre style="margin: 0;"> <span id="LC599" class="line" lang="plaintext"> system("rm -f ".$opts->fafile().".pid");</span>
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<pre style="margin: 0;"> <span id="LC600" class="line" lang="plaintext">}</span>
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<pre style="margin: 0;"> <span id="LC601" class="line" lang="plaintext"></span>
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