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<h3>
Andreas Tille pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/kalign">Debian Med / kalign</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/kalign/-/commit/7ebdac5ad2b6823ab8972de5e525d333aa9b4d51">7ebdac5a</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2021-10-01T13:15:34+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 3.3.1</pre>
</li>
</ul>
<h4>11 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#00fe7828d56d7a3ee4030d6cea057cf13f50e70c">
ChangeLog
</a>
</li>
<li class="file-stats">
<a href="#69e27356ef629022720d868ab0c0e3394775b6c1">
README
</a>
</li>
<li class="file-stats">
<a href="#87db583be5c13c1f7b3c958b10e03d67b6a2ca06">
configure.ac
</a>
</li>
<li class="file-stats">
<a href="#ab0941e3fc6a829a4eb4706cc6d4fdc756eeb009">
dev/run_io_test.sh
</a>
</li>
<li class="file-stats">
<a href="#82d29b0dd902d85c9fb73cdb1ad71d7f9202ac8e">
src/alignment_parameters.c
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<li class="file-stats">
<a href="#961120526b478238a46befc41e1d21c2d1e223b5">
src/alignment_parameters.h
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<li class="file-stats">
<a href="#70343f735a1dedf8224cdebdae76f63463327e15">
src/aln_run.c
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<li class="file-stats">
<a href="#830464862debacd7cdfde9fb2e1e7dae90d05037">
src/run_kalign.c
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</li>
<li class="file-stats">
<a href="#1fcac97a50c178927c95e2825634ac351353343b">
src/rwalign.c
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<li class="file-stats">
<a href="#fc361d05a36c44f4d7065a69f501c01dd8628237">
src/weave_alignment.c
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<li class="file-stats">
<a href="#86c2e400778487ece9407ed83a97fc3900542320">
src/weave_alignment.h
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<h4>Changes:</h4>
<li id="00fe7828d56d7a3ee4030d6cea057cf13f50e70c">
<a href="https://salsa.debian.org/med-team/kalign/-/commit/7ebdac5ad2b6823ab8972de5e525d333aa9b4d51#00fe7828d56d7a3ee4030d6cea057cf13f50e70c"><strong>ChangeLog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">2021-04-16 Timo Lassmann <timo.lassmann@telethonkids.org.au></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * version 3.3.1 - Bug Fix</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> The previous version kalign checked the top 50 sequences in inputs to determine</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> whether the sequences are aligned or not. If the first 50 sequences are not aligned,</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> but following sequences contain gaps (or other characters!) kalign can crash. In this</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> version (3.3.1) kalign checks all sequences, thereby avoiding this issue.</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> To alert users to the situation described above and to warn users about the presence of</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> odd characters, kalign now produces a warning message like this:</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"> [Date Time] : LOG : Start io tests.</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> [Date Time] : LOG : reading: dev/data/a2m.good.1</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> [Date Time] : LOG : Detected protein sequences.</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> [Date Time] : WARNING : -------------------------------------------- (rwalign.c line 505)</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"> [Date Time] : WARNING : The input sequences contain gap characters: (rwalign.c line 506)</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"> [Date Time] : WARNING : "-" : 36 found (rwalign.c line 510)</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"> [Date Time] : WARNING : BUT the sequences do not seem to be aligned! (rwalign.c line 514)</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"> [Date Time] : WARNING : (rwalign.c line 515)</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"> [Date Time] : WARNING : Kalign will remove the gap characters and (rwalign.c line 516)</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"> [Date Time] : WARNING : align the sequences. (rwalign.c line 517)</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"> [Date Time] : WARNING : -------------------------------------------- (rwalign.c line 518)</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext">2020-11-06 Timo Lassmann <timo.lassmann@telethonkids.org.au></span>
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2
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24
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext"> * version 3.3 - Threading and more</span>
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<a href="https://salsa.debian.org/med-team/kalign/-/commit/7ebdac5ad2b6823ab8972de5e525d333aa9b4d51#69e27356ef629022720d868ab0c0e3394775b6c1"><strong>README</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">-----------------------------------------------------------------------</span>
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2
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext"> Kalign version 2.03, Copyright (C) 2006 Timo Lassmann</span>
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3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext"> http://msa.cgb.ki.se/</span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext"> timolassmann@gmail.com</span>
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6
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext"></span>
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7
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext"> This program is free software; you can redistribute it and/or modify</span>
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8
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext"> it under the terms of the GNU General Public License as published by</span>
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9
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext"> the Free Software Foundation; either version 2 of the License, or</span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext"> any later version.</span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext"> This program is distributed in the hope that it will be useful,</span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext"> but WITHOUT ANY WARRANTY; without even the implied warranty of</span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext"> MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the</span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="plaintext"> GNU General Public License for more details.</span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="plaintext"> You should have received a copy of the GNU General Public License</span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="plaintext"> along with this program; if not, write to the Free Software</span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="plaintext"> Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA</span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="plaintext"> </span>
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21
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="plaintext"> A copy of this license is in the COPYING file.</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"> Kalign - a multiple sequence alignment program</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> Copyright 2006, 2019, 2020, 2021 Timo Lassmann</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> This file is part of kalign.</span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> Kalign is free software: you can redistribute it and/or modify</span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> it under the terms of the GNU General Public License as published by</span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> the Free Software Foundation, either version 3 of the License, or</span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> (at your option) any later version.</span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> This program is distributed in the hope that it will be useful,</span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> but WITHOUT ANY WARRANTY; without even the implied warranty of</span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"> MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the</span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"> GNU General Public License for more details.</span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"> You should have received a copy of the GNU General Public License</span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"> along with this program. If not, see <https://www.gnu.org/licenses/>.</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext">-----------------------------------------------------------------------</span>
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23
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="plaintext">Installation:</span>
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24
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext"></span>
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25
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="plaintext">% ./configure </span>
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26
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="plaintext">% make</span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">Kalign is a fast multiple sequence alignment program for biological sequences.</span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"></span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">1) Installation</span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext"></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">1.1) Release Tarball</span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext"></span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">Download tarball from [releases](https://github.com/TimoLassmann/kalign/releases). Then:</span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext"></span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">tar -zxvf kalign-<version>.tar.gz</span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">cd kalign-<version></span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">./autogen.sh</span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext">./configure</span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext">make</span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext">make check</span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext">make install</span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext"></span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext"></span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext">1.2) Homebrew</span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext"></span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext">brew install brewsci/bio/kalign</span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext"></span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext">1.3) Developer version</span>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext"></span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext">git clone https://github.com/TimoLassmann/kalign.git</span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext">cd kalign</span>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext">./autogen.sh</span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext">./configure</span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext">make</span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext">make check</span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext">make install</span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext"></span>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext"></span>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext">1.4) on macOS, install [brew](https://brew.sh/) then:</span>
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="plaintext"></span>
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="plaintext">brew install libtool</span>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="plaintext">brew install automake</span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="plaintext">git clone https://github.com/TimoLassmann/kalign.git</span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="plaintext">cd kalign</span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="plaintext">./autogen.sh</span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="plaintext">./configure</span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="plaintext">make</span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="plaintext">make check</span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="plaintext">make install</span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="plaintext"></span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="plaintext"></span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="plaintext">2) Usage</span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="plaintext"></span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="plaintext">Usage: kalign -i <seq file> -o <out aln></span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="plaintext"></span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="plaintext">Options:</span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="plaintext"></span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="plaintext"> --format : Output format. [Fasta]</span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="plaintext"> --reformat : Reformat existing alignment. [NA]</span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="plaintext"> --version : Print version and exit</span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="plaintext">Kalign expects the input to be a set of unaligned sequences in fasta format or aligned sequences in aligned fasta, MSF or clustal format. Kalign automatically detects whether the input sequences are protein, RNA or DNA.</span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="plaintext"></span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="plaintext">Since version 3.2.0 kalign supports passing sequence in via stdin and support alignment of sequences from multiple files.</span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="plaintext"></span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="plaintext">3) Examples</span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="plaintext"></span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="plaintext">Passing sequences via stdin:</span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="plaintext"></span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="plaintext"> cat input.fa | kalign -f fasta > out.afa</span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="plaintext"></span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="plaintext">Combining multiple input files:</span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="plaintext"> kalign seqsA.fa seqsB.fa seqsC.fa -f fasta > combined.afa</span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="plaintext"></span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="plaintext">Align sequences and output the alignment in MSF format:</span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="plaintext"></span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="plaintext"> kalign -i BB11001.tfa -f msf -o out.msf</span>
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27
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95
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<pre style="margin: 0;"> <span id="LC95" class="line" lang="plaintext"></span>
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28
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="plaintext"><span class="idiff left right">and as roo</span>t:</span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="plaintext"><span class="idiff left right">Align sequences and output the alignment in clustal forma</span>t:</span>
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29
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97
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<pre style="margin: 0;"> <span id="LC97" class="line" lang="plaintext"></span>
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30
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="plaintext"><span class="idiff left right">% make install</span></span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="plaintext"><span class="idiff left right"> kalign -i BB11001.tfa -f clu -o out.clu</span></span>
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31
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99
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="plaintext"></span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="plaintext">Re-align sequences in an existing alignment:</span>
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32
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101
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<pre style="margin: 0;"> <span id="LC101" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="plaintext"><span class="idiff left right">Usage:</span></span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="plaintext"><span class="idiff left right"> kalign -i BB11001.msf -o out.afa</span></span>
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103
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="plaintext"> kalign [Options] infile.fasta outfile.fasta</span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="plaintext"> or:</span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="plaintext"> kalign [Options] -i infile.fasta -o outfile.fasta</span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="plaintext"> or:</span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="plaintext"> kalign [Options] < infile.fasta > outfile.fasta</span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="plaintext">Reformat existing alignment:</span>
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<pre style="margin: 0;"> <span id="LC105" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="plaintext"> Options:</span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="plaintext"> type: kalign -h </span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="plaintext"> </span></pre>
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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">\ No newline at end of file</td>
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="plaintext"> kalign -i BB11001.msf -r afa -o out.afa</span></pre>
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<a href="https://salsa.debian.org/med-team/kalign/-/commit/7ebdac5ad2b6823ab8972de5e525d333aa9b4d51#87db583be5c13c1f7b3c958b10e03d67b6a2ca06"><strong>configure.ac</strong></a>
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1
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">AC_INIT(kalign, 3.3)</span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">AC_INIT(kalign, 3.3<span class="idiff left right">.1</span>)</span>
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2
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"></span>
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3
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">#AC_CONFIG_AUX_DIR([.])</span>
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4
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"></span>
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<a href="https://salsa.debian.org/med-team/kalign/-/commit/7ebdac5ad2b6823ab8972de5e525d333aa9b4d51#ab0941e3fc6a829a4eb4706cc6d4fdc756eeb009"><strong>dev/run_io_test.sh</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -18,5 +18,4 @@ do</td>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">printf</span> <span class="s2" style="color: #d14;">"with ERROR </span><span class="nv" style="color: #008080;">$status</span><span class="s2" style="color: #d14;"> and Message:</span><span class="se" style="color: #d14;">\n\n</span><span class="nv" style="color: #008080;">$error</span><span class="se" style="color: #d14;">\n\n</span><span class="s2" style="color: #d14;">"</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">exit </span>1<span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="shell"> <span class="k" style="font-weight: 600;">fi</span></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="shell"><span class="k" style="font-weight: 600;">done</span></span></pre>
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<a href="https://salsa.debian.org/med-team/kalign/-/commit/7ebdac5ad2b6823ab8972de5e525d333aa9b4d51#82d29b0dd902d85c9fb73cdb1ad71d7f9202ac8e"><strong>src/alignment_parameters.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">@@ -30,7 +30,7 @@ int set_param_number(struct aln_param* ap,int L, int sel);</td>
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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;">int</span> <span class="nf" style="color: #900; font-weight: 600;">new_aln_matrices</span><span class="p">(</span><span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">aln_param</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">ap</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">init_ap</span><span class="p">(</span><span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">aln_param</span><span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">aln_param</span><span class="p">,</span> <span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">parameters</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">param</span><span class="p">,</span><span class="idiff left"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">int</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">numseq</span></span><span class="p"><span class="idiff right">,</span></span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">L</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">init_ap</span><span class="p">(</span><span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">aln_param</span><span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">aln_param</span><span class="p">,</span> <span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">parameters</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">param</span><span class="p">,</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">L</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="c"><span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="c"> <span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">aln_param</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">ap</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC36" 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>
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<a href="https://salsa.debian.org/med-team/kalign/-/commit/7ebdac5ad2b6823ab8972de5e525d333aa9b4d51#961120526b478238a46befc41e1d21c2d1e223b5"><strong>src/alignment_parameters.h</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -55,6 +55,6 @@ struct aln_param{</td>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="c"><span class="p">};</span></span>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="c"><span class="k" style="font-weight: 600;">extern</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">init_ap</span><span class="p">(</span><span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">aln_param</span><span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">aln_param</span><span class="p">,</span> <span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">parameters</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">param</span><span class="p">,</span><span class="idiff left"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">int</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">numseq</span></span><span class="p"><span class="idiff right">,</span></span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">L</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="c"><span class="k" style="font-weight: 600;">extern</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">init_ap</span><span class="p">(</span><span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">aln_param</span><span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">aln_param</span><span class="p">,</span> <span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">parameters</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">param</span><span class="p">,</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">L</span><span class="p">);</span></span>
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59
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="c"><span class="k" style="font-weight: 600;">extern</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">free_ap</span><span class="p">(</span><span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">aln_param</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">ap</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span></pre>
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<a href="https://salsa.debian.org/med-team/kalign/-/commit/7ebdac5ad2b6823ab8972de5e525d333aa9b4d51#70343f735a1dedf8224cdebdae76f63463327e15"><strong>src/aln_run.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">@@ -868,6 +868,7 @@ int do_align_serial(struct msa* msa,struct aln_tasks* t,struct aln_mem* m, int t</td>
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868
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868
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<pre style="margin: 0;"> <span id="LC868" class="line" lang="c"> <span class="n" style="color: #333;">MFREE</span><span class="p">(</span><span class="n" style="color: #333;">t</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">profile</span><span class="p">[</span><span class="n" style="color: #333;">b</span><span class="p">]);</span></span>
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869
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869
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<pre style="margin: 0;"> <span id="LC869" class="line" lang="c"></span>
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870
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870
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<pre style="margin: 0;"> <span id="LC870" class="line" lang="c"> <span class="n" style="color: #333;">t</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">profile</span><span class="p">[</span><span class="n" style="color: #333;">c</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tmp</span><span class="p">;</span></span>
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871
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<pre style="margin: 0;">+<span id="LC871" class="line" lang="c"></span>
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872
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<pre style="margin: 0;"> <span id="LC872" class="line" lang="c"> <span class="n" style="color: #333;">RUN</span><span class="p">(</span><span class="n" style="color: #333;">make_seq</span><span class="p">(</span><span class="n" style="color: #333;">msa</span><span class="p">,</span><span class="n" style="color: #333;">a</span><span class="p">,</span><span class="n" style="color: #333;">b</span><span class="p">,</span><span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">path</span><span class="p">));</span></span>
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872
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873
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<pre style="margin: 0;"> <span id="LC873" class="line" lang="c"></span>
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874
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<pre style="margin: 0;"> <span id="LC874" class="line" lang="c"> <span class="n" style="color: #333;">msa</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">plen</span><span class="p">[</span><span class="n" style="color: #333;">c</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">m</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">path</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></span>
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<a href="https://salsa.debian.org/med-team/kalign/-/commit/7ebdac5ad2b6823ab8972de5e525d333aa9b4d51#830464862debacd7cdfde9fb2e1e7dae90d05037"><strong>src/run_kalign.c</strong></a>
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/*</span></span>
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2
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> Kalign - a multiple sequence alignment program</span></span>
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3
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> Copyright 2006, 2019, 2020 Timo Lassmann</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;"> Copyright 2006, 2019, 2020<span class="idiff left right">, 2021</span> Timo Lassmann</span></span>
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="c"></span>
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> This file is part of kalign.</span></span>
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7
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7
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="c"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="132" style="width: 35px; color: rgba(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="132" style="width: 35px; color: rgba(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">@@ -132,7 +132,7 @@ int print_kalign_header(void)</td>
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132
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132
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<pre style="margin: 0;"> <span id="LC132" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stdout</span><span class="p">,</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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133
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133
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<pre style="margin: 0;"> <span id="LC133" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stdout</span><span class="p">,</span><span class="s" style="color: #d14;">"Kalign (%s)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">PACKAGE_VERSION</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC134" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stdout</span><span class="p">,</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC135" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stdout</span><span class="p">,</span><span class="s" style="color: #d14;">"Copyright (C) 2006,2019,2020 Timo Lassmann</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stdout</span><span class="p">,</span><span class="s" style="color: #d14;">"Copyright (C) 2006,2019,2020<span class="idiff left right">,2021</span> Timo Lassmann</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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136
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<pre style="margin: 0;"> <span id="LC136" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stdout</span><span class="p">,</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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137
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<pre style="margin: 0;"> <span id="LC137" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stdout</span><span class="p">,</span><span class="s" style="color: #d14;">"This program comes with ABSOLUTELY NO WARRANTY; for details type:</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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138
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138
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<pre style="margin: 0;"> <span id="LC138" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stdout</span><span class="p">,</span><span class="s" style="color: #d14;">"`kalign -showw'.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="520" style="width: 35px; color: rgba(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">@@ -520,7 +520,7 @@ int run_kalign(struct parameters* param)</td>
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<pre style="margin: 0;"> <span id="LC520" class="line" lang="c"> <span class="p">}</span></span>
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521
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<pre style="margin: 0;"> <span id="LC521" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC522" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* allocate aln parameters */</span></span>
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<pre style="margin: 0;">-<span id="LC523" class="line" lang="c"> <span class="n" style="color: #333;">RUN</span><span class="p">(</span><span class="n" style="color: #333;">init_ap</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">ap</span><span class="p">,</span><span class="n" style="color: #333;">param</span><span class="p">,</span><span class="n" style="color: #333;">msa</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;"><span class="idiff left">numseq</span></span><span class="p"><span class="idiff">,</span></span><span class="n" style="color: #333;"><span class="idiff">msa</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">-></span></span><span class="n" style="color: #333;">L</span> <span class="p">));</span></span>
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<pre style="margin: 0;">+<span id="LC523" class="line" lang="c"> <span class="n" style="color: #333;">RUN</span><span class="p">(</span><span class="n" style="color: #333;">init_ap</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">ap</span><span class="p">,</span><span class="n" style="color: #333;">param</span><span class="p">,</span><span class="n" style="color: #333;">msa</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">L</span> <span class="p">));</span></span>
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<pre style="margin: 0;"> <span id="LC524" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC525" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">param</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">dump_internal</span><span class="p">){</span></span>
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<pre style="margin: 0;"> <span id="LC526" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">s</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="555" style="width: 35px; color: rgba(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">@@ -555,7 +555,7 @@ int run_kalign(struct parameters* param)</td>
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<pre style="margin: 0;"> <span id="LC555" class="line" lang="c"> <span class="n" style="color: #333;">RUN</span><span class="p">(</span><span class="n" style="color: #333;">convert_msa_to_internal</span><span class="p">(</span><span class="n" style="color: #333;">msa</span><span class="p">,</span> <span class="n" style="color: #333;">ALPHA_ambigiousPROTEIN</span><span class="p">));</span></span>
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556
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556
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<pre style="margin: 0;"> <span id="LC556" class="line" lang="c"> <span class="p">}</span></span>
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557
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<pre style="margin: 0;"> <span id="LC557" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* allocate aln parameters */</span></span>
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558
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<pre style="margin: 0;">-<span id="LC558" class="line" lang="c"> <span class="n" style="color: #333;">RUN</span><span class="p">(</span><span class="n" style="color: #333;">init_ap</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">ap</span><span class="p">,</span><span class="n" style="color: #333;">param</span><span class="p">,</span><span class="n" style="color: #333;">msa</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;"><span class="idiff left">numseq</span></span><span class="p"><span class="idiff">,</span></span><span class="n" style="color: #333;"><span class="idiff">msa</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">-></span></span><span class="n" style="color: #333;">L</span> <span class="p">));</span></span>
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558
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<pre style="margin: 0;">+<span id="LC558" class="line" lang="c"> <span class="n" style="color: #333;">RUN</span><span class="p">(</span><span class="n" style="color: #333;">init_ap</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">ap</span><span class="p">,</span><span class="n" style="color: #333;">param</span><span class="p">,</span><span class="n" style="color: #333;">msa</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">L</span> <span class="p">));</span></span>
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<pre style="margin: 0;"> <span id="LC559" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC560" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* Start alignment stuff */</span></span>
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<pre style="margin: 0;"> <span id="LC561" class="line" lang="c"> <span class="n" style="color: #333;">DECLARE_TIMER</span><span class="p">(</span><span class="n" style="color: #333;">t1</span><span class="p">);</span></span>
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<a href="https://salsa.debian.org/med-team/kalign/-/commit/7ebdac5ad2b6823ab8972de5e525d333aa9b4d51#1fcac97a50c178927c95e2825634ac351353343b"><strong>src/rwalign.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">@@ -65,29 +65,29 @@ struct out_line{</td>
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">aln_unknown_warning_message</span><span class="p">(</span><span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">msa</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">msa</span><span class="p">);</span></span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">read_fasta</span><span class="p">(</span><span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">in_buffer</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">b</span><span class="p">,</span> <span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">msa</span><span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">msa</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">read_msf</span><span class="p">(</span><span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">in_buffer</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">b</span><span class="p">,</span> <span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">msa</span><span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">msa</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">read_clu</span><span class="p">(</span><span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">in_buffer</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">b</span><span class="p">,</span> <span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">msa</span><span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">msa</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">read_fasta</span><span class="p">(</span><span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">in_buffer</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">b</span><span class="p">,</span> <span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">msa</span><span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">msa</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">read_msf</span><span class="p">(</span><span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">in_buffer</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">b</span><span class="p">,</span> <span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">msa</span><span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">msa</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">read_clu</span><span class="p">(</span><span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">in_buffer</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">b</span><span class="p">,</span> <span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">msa</span><span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">msa</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC73" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">write_msa_fasta</span><span class="p">(</span><span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">msa</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">msa</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;">outfile</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC74" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">write_msa_clustal</span><span class="p">(</span><span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">msa</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">msa</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;">outfile</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC75" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">write_msa_msf</span><span class="p">(</span><span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">msa</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">msa</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;">outfile</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">write_msa_fasta</span><span class="p">(</span><span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">msa</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">msa</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;">outfile</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">write_msa_clustal</span><span class="p">(</span><span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">msa</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">msa</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;">outfile</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">write_msa_msf</span><span class="p">(</span><span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">msa</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">msa</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;">outfile</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/* memory functions */</span></span>
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<pre style="margin: 0;">-<span id="LC78" class="line" lang="c"><span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">msa</span><span class="o" style="font-weight: 600;">*</span> <span class="nf" style="color: #900; font-weight: 600;">alloc_msa</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">void</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC79" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">resize_msa</span><span class="p">(</span><span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">msa</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">msa</span><span class="p">);</span></span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="c"><span class="k" style="font-weight: 600;"><span class="idiff left">static</span></span><span class="idiff right"> </span><span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">msa</span><span class="o" style="font-weight: 600;">*</span> <span class="nf" style="color: #900; font-weight: 600;">alloc_msa</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">void</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="c"><span class="k" style="font-weight: 600;"><span class="idiff left">static</span></span><span class="idiff right"> </span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">resize_msa</span><span class="p">(</span><span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">msa</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">msa</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC82" class="line" lang="c"><span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">msa_seq</span><span class="o" style="font-weight: 600;">*</span> <span class="nf" style="color: #900; font-weight: 600;">alloc_msa_seq</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">void</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC83" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">resize_msa_seq</span><span class="p">(</span><span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">msa_seq</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="LC84" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">free_msa_seq</span><span class="p">(</span><span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">msa_seq</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="LC82" class="line" lang="c"><span class="k" style="font-weight: 600;"><span class="idiff left">static</span></span><span class="idiff right"> </span><span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">msa_seq</span><span class="o" style="font-weight: 600;">*</span> <span class="nf" style="color: #900; font-weight: 600;">alloc_msa_seq</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">void</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="c"><span class="k" style="font-weight: 600;"><span class="idiff left">static</span></span><span class="idiff right"> </span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">resize_msa_seq</span><span class="p">(</span><span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">msa_seq</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="LC84" class="line" lang="c"><span class="k" style="font-weight: 600;"><span class="idiff left">static</span></span><span class="idiff right"> </span><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">free_msa_seq</span><span class="p">(</span><span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">msa_seq</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="LC85" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC87" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC88" class="line" lang="c"><span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">line_buffer</span><span class="o" style="font-weight: 600;">*</span> <span class="nf" style="color: #900; font-weight: 600;">alloc_line_buffer</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">max_line_len</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC89" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">resize_line_buffer</span><span class="p">(</span><span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">line_buffer</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">lb</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC90" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">free_line_buffer</span><span class="p">(</span><span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">line_buffer</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">lb</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="c"><span class="k" style="font-weight: 600;"><span class="idiff left">static</span></span><span class="idiff right"> </span><span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">line_buffer</span><span class="o" style="font-weight: 600;">*</span> <span class="nf" style="color: #900; font-weight: 600;">alloc_line_buffer</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">max_line_len</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="c"><span class="k" style="font-weight: 600;"><span class="idiff left">static</span></span><span class="idiff right"> </span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">resize_line_buffer</span><span class="p">(</span><span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">line_buffer</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">lb</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="c"><span class="k" style="font-weight: 600;"><span class="idiff left">static</span></span><span class="idiff right"> </span><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">free_line_buffer</span><span class="p">(</span><span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">line_buffer</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">lb</span><span class="p">);</span></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="LC92" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">read_file_stdin</span><span class="p">(</span><span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">in_buffer</span><span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">buffer</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;">infile</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC93" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">alloc_in_buffer</span><span class="p">(</span><span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">in_buffer</span><span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">buffer</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">n</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="106" style="width: 35px; color: rgba(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="106" style="width: 35px; color: rgba(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">@@ -106,8 +106,6 @@ static int GCGMultchecksum(struct msa* msa);</td>
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<pre style="margin: 0;"> <span id="LC106" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/* Taken from squid library by Sean Eddy */</span></span>
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<pre style="margin: 0;"> <span id="LC107" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">GCGchecksum</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;">len</span><span class="p">);</span></span>
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108
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<pre style="margin: 0;"> <span id="LC108" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC109" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC110" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC109" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">sort_by_name</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">a</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">b</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC110" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">sort_by_chksum</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">a</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">b</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC111" class="line" lang="c"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="248" style="width: 35px; color: rgba(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="246" style="width: 35px; color: rgba(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">@@ -248,7 +246,6 @@ int read_input(char* infile,struct msa** msa)</td>
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<pre style="margin: 0;"> <span id="LC246" class="line" lang="c"> <span class="n" style="color: #333;">STOP_TIMER</span><span class="p">(</span><span class="n" style="color: #333;">timer</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC247" class="line" lang="c"> <span class="n" style="color: #333;">GET_TIMING</span><span class="p">(</span><span class="n" style="color: #333;">timer</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC248" class="line" lang="c"> <span class="n" style="color: #333;">DESTROY_TIMER</span><span class="p">(</span><span class="n" style="color: #333;">timer</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC251" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">//LOG_MSG("Done reading input sequences in %f seconds.", GET_TIMING(timer));</span></span>
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<pre style="margin: 0;"> <span id="LC249" class="line" lang="c"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">msa</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">m</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC250" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">OK</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC251" class="line" lang="c"><span class="nl">ERROR:</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">@@ -465,7 +462,8 @@ int detect_aligned(struct msa* msa)</td>
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<pre style="margin: 0;"> <span id="LC462" class="line" lang="c"> <span class="n" style="color: #333;">min_len</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">INT32_MAX</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC463" class="line" lang="c"> <span class="n" style="color: #333;">max_len</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC464" class="line" lang="c"> <span class="n" style="color: #333;">gaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC468" class="line" lang="c"> <span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">MACRO_MIN</span><span class="p">(</span><span class="mi" style="color: #099;">50</span><span class="p">,</span> <span class="n" style="color: #333;">msa</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">numseq</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC465" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* n = MACRO_MIN(50, msa->numseq); */</span></span>
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<pre style="margin: 0;">+<span id="LC466" class="line" lang="c"> <span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">msa</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">numseq</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC467" 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;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">n</span><span class="p">;</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">){</span></span>
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<pre style="margin: 0;"> <span id="LC468" class="line" lang="c"> <span class="n" style="color: #333;">l</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC469" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</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="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">msa</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">sequences</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">len</span><span class="p">;</span><span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">++</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">@@ -480,12 +478,17 @@ int detect_aligned(struct msa* msa)</td>
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<pre style="margin: 0;"> <span id="LC478" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">min_len</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">max_len</span><span class="p">){</span> <span class="cm" style="color: #998; font-style: italic;">/* sequences have gaps and total length is identical - clearly aligned */</span></span>
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<pre style="margin: 0;"> <span id="LC479" class="line" lang="c"> <span class="n" style="color: #333;">msa</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">aligned</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ALN_STATUS_ALIGNED</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC480" class="line" lang="c"> <span class="p">}</span><span class="k" style="font-weight: 600;">else</span><span class="p">{</span> <span class="cm" style="color: #998; font-style: italic;">/* odd there are gaps but total length differs - unknown status */</span></span>
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<pre style="margin: 0;">+<span id="LC481" class="line" lang="c"> <span class="n" style="color: #333;">aln_unknown_warning_message</span><span class="p">(</span><span class="n" style="color: #333;">msa</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC483" class="line" lang="c"> <span class="n" style="color: #333;">msa</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">aligned</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ALN_STATUS_UNKNOWN</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC484" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC485" class="line" lang="c"> <span class="p">}</span><span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC486" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">min_len</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">max_len</span><span class="p">){</span> <span class="cm" style="color: #998; font-style: italic;">/* no gaps and sequences have same length. Can' tell if they are aligned */</span></span>
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<pre style="margin: 0;">+<span id="LC487" class="line" lang="c"> <span class="n" style="color: #333;">aln_unknown_warning_message</span><span class="p">(</span><span class="n" style="color: #333;">msa</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC488" class="line" lang="c"> <span class="n" style="color: #333;">msa</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">aligned</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ALN_STATUS_UNKNOWN</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC489" class="line" lang="c"> <span class="p">}</span><span class="k" style="font-weight: 600;">else</span><span class="p">{</span> <span class="cm" style="color: #998; font-style: italic;">/* No gaps and sequences have different lengths - unaligned */</span></span>
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<pre style="margin: 0;"> <span id="LC492" class="line" lang="c"> <span class="n" style="color: #333;">msa</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">aligned</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ALN_STATUS_UNALIGNED</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC493" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC494" 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">@@ -493,15 +496,36 @@ int detect_aligned(struct msa* msa)</td>
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<pre style="margin: 0;"> <span id="LC496" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">OK</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC497" class="line" lang="c"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC498" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC499" class="line" lang="c"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">aln_unknown_warning_message</span><span class="p">(</span><span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">msa</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">msa</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC500" class="line" lang="c"><span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC501" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC502" class="line" lang="c"> <span class="n" style="color: #333;">WARNING_MSG</span><span class="p">(</span><span class="s" style="color: #d14;">"--------------------------------------------"</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC503" class="line" lang="c"> <span class="n" style="color: #333;">WARNING_MSG</span><span class="p">(</span><span class="s" style="color: #d14;">"The input sequences contain gap characters: "</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC504" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC505" 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;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">128</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>
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506
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<pre style="margin: 0;">+<span id="LC506" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">msa</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">letter_freq</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">ispunct</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">)){</span></span>
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507
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<pre style="margin: 0;">+<span id="LC507" class="line" lang="c"> <span class="n" style="color: #333;">WARNING_MSG</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">%c</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;"> : %4d found "</span><span class="p">,</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="p">)</span><span class="n" style="color: #333;">i</span><span class="p">,</span><span class="n" style="color: #333;">msa</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">letter_freq</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="p">);</span></span>
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508
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<pre style="margin: 0;">+<span id="LC508" class="line" lang="c"> <span class="p">}</span></span>
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509
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<pre style="margin: 0;">+<span id="LC509" class="line" lang="c"> <span class="p">}</span></span>
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510
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<pre style="margin: 0;">+<span id="LC510" class="line" lang="c"></span>
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511
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<pre style="margin: 0;">+<span id="LC511" class="line" lang="c"> <span class="n" style="color: #333;">WARNING_MSG</span><span class="p">(</span><span class="s" style="color: #d14;">"BUT the sequences do not seem to be aligned!"</span><span class="p">);</span></span>
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512
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<pre style="margin: 0;">+<span id="LC512" class="line" lang="c"> <span class="n" style="color: #333;">WARNING_MSG</span><span class="p">(</span><span class="s" style="color: #d14;">" "</span><span class="p">);</span></span>
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513
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<pre style="margin: 0;">+<span id="LC513" class="line" lang="c"> <span class="n" style="color: #333;">WARNING_MSG</span><span class="p">(</span><span class="s" style="color: #d14;">"Kalign will remove the gap characters and "</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="514" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
514
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<pre style="margin: 0;">+<span id="LC514" class="line" lang="c"> <span class="n" style="color: #333;">WARNING_MSG</span><span class="p">(</span><span class="s" style="color: #d14;">"align the sequences. "</span><span class="p">);</span></span>
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515
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<pre style="margin: 0;">+<span id="LC515" class="line" lang="c"> <span class="n" style="color: #333;">WARNING_MSG</span><span class="p">(</span><span class="s" style="color: #d14;">"--------------------------------------------"</span><span class="p">);</span></span>
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516
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<pre style="margin: 0;">+<span id="LC516" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">OK</span><span class="p">;</span></span>
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517
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<pre style="margin: 0;">+<span id="LC517" class="line" lang="c"><span class="p">}</span></span>
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518
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<pre style="margin: 0;">+<span id="LC518" class="line" lang="c"></span>
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519
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<pre style="margin: 0;">+<span id="LC519" class="line" lang="c"></span>
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496
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520
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<pre style="margin: 0;"> <span id="LC520" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/* Checks if sequence names are duplicated */</span></span>
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497
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521
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<pre style="margin: 0;"> <span id="LC521" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/* Checks if sequences are duplicated */</span></span>
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498
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522
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<pre style="margin: 0;"> <span id="LC522" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">run_extra_checks_on_msa</span><span class="p">(</span><span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">msa</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">msa</span><span class="p">)</span></span>
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499
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523
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<pre style="margin: 0;"> <span id="LC523" class="line" lang="c"><span class="p">{</span></span>
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500
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524
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<pre style="margin: 0;"> <span id="LC524" class="line" lang="c"> <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;">tmp_name</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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501
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<pre style="margin: 0;">-<span id="LC501" class="line" lang="c"> <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;">tmp_ptr</span><span class="p">;</span></span>
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525
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<pre style="margin: 0;">+<span id="LC525" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;"><span class="idiff left">/* </span>char* tmp_ptr;<span class="idiff right"> */</span></span></span>
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502
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526
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<pre style="margin: 0;"> <span id="LC526" class="line" lang="c"> <span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">sort_struct_name_chksum</span><span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">a</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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503
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527
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<pre style="margin: 0;"> <span id="LC527" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span><span class="p">;</span></span>
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504
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<pre style="margin: 0;">-<span id="LC504" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">j</span><span class="p">;</span></span>
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528
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<pre style="margin: 0;">+<span id="LC528" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;"><span class="idiff left">/* </span>int j;<span class="idiff right"> */</span></span></span>
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505
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529
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<pre style="margin: 0;"> <span id="LC529" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">c</span><span class="p">;</span></span>
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506
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530
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<pre style="margin: 0;"> <span id="LC530" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">l</span><span class="p">;</span></span>
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507
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531
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<pre style="margin: 0;"> <span id="LC531" class="line" lang="c"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1174" style="width: 35px; color: rgba(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="1198" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1174,50 +1198,30 @@ int read_clu(struct in_buffer* b , struct msa** m)</td>
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1174
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1198
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<pre style="margin: 0;"> <span id="LC1198" class="line" lang="c"><span class="p">{</span></span>
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1175
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1199
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<pre style="margin: 0;"> <span id="LC1199" class="line" lang="c"> <span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">msa</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">msa</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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1176
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1200
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<pre style="margin: 0;"> <span id="LC1200" class="line" lang="c"> <span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">msa_seq</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">seq_ptr</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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1177
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<pre style="margin: 0;">-<span id="LC1177" class="line" lang="c"><span class="idiff left"> </span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right">//FILE* f_ptr = NULL;</span></span></span>
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1201
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<pre style="margin: 0;">+<span id="LC1201" class="line" lang="c"></span>
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1178
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1202
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<pre style="margin: 0;"> <span id="LC1202" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">line</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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1179
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<pre style="margin: 0;">-<span id="LC1179" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">//size_t b_len = 0;</span></span>
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1180
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<pre style="margin: 0;">-<span id="LC1180" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">//ssize_t nread;</span></span>
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1181
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1203
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<pre style="margin: 0;"> <span id="LC1203" 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>
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1182
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1204
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<pre style="margin: 0;"> <span id="LC1204" class="line" lang="c"> <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;">p</span><span class="p">;</span></span>
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1183
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1205
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<pre style="margin: 0;"> <span id="LC1205" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">active_seq</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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1184
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1206
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<pre style="margin: 0;"> <span id="LC1206" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">line_len</span><span class="p">;</span></span>
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1185
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1207
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<pre style="margin: 0;"> <span id="LC1207" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nl</span><span class="p">,</span><span class="n" style="color: #333;">ni</span><span class="p">;</span></span>
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1186
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<pre style="margin: 0;">-<span id="LC1186" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* sanity checks */</span></span>
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1187
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<pre style="margin: 0;">-<span id="LC1187" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">//if(!my_file_exists(infile)){</span></span>
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1188
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<pre style="margin: 0;">-<span id="LC1188" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">//ERROR_MSG("File: %s does not exist.",infile);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1189" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1189
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<td class="new_line diff-line-num old" data-linenumber="1208" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1189" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">//}</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1190" style="width: 35px; color: rgba(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="1208" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1208
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<pre style="margin: 0;">+<span id="LC1208" class="line" lang="c"></span>
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<td class="old_line diff-line-num" data-linenumber="1190" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1190
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<td class="new_line diff-line-num" data-linenumber="1209" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1209
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<pre style="margin: 0;"> <span id="LC1209" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">msa</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">){</span></span>
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<td class="old_line diff-line-num" data-linenumber="1191" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1191
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<td class="new_line diff-line-num" data-linenumber="1210" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1210
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<pre style="margin: 0;"> <span id="LC1210" class="line" lang="c"> <span class="n" style="color: #333;">msa</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alloc_msa</span><span class="p">();</span></span>
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<td class="old_line diff-line-num" data-linenumber="1192" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1192
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<td class="new_line diff-line-num" data-linenumber="1211" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1211
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<pre style="margin: 0;"> <span id="LC1211" class="line" lang="c"> <span class="p">}</span></span>
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<td class="old_line diff-line-num" data-linenumber="1193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1193
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<td class="new_line diff-line-num" data-linenumber="1212" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1212
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<pre style="margin: 0;"> <span id="LC1212" class="line" lang="c"></span>
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<td class="old_line diff-line-num old" data-linenumber="1194" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1194
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<td class="new_line diff-line-num old" data-linenumber="1213" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1194" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">//RUNP(f_ptr = fopen(infile, "r"));</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1195" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1195
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<td class="new_line diff-line-num old" data-linenumber="1213" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1195" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">//LOG_MSG("GAGA");</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1196" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1196
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<td class="new_line diff-line-num old" data-linenumber="1213" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1196" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* scan through first line header */</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1197" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1197
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<td class="new_line diff-line-num old" data-linenumber="1213" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1197" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">//while(fgets(line, BUFFER_LEN, f_ptr)){</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1198" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1198
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<td class="new_line diff-line-num old" data-linenumber="1213" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1198" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">//while ((nread = getline(&line, &b_len, f_ptr)) != -1){</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1199" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1199
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<td class="new_line diff-line-num old" data-linenumber="1213" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1199" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">//fprintf(stdout,"LINE: %s", line);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1200" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1200
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<td class="new_line diff-line-num old" data-linenumber="1213" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1200" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">//line_len = strnlen(line, BUFFER_LEN);</span></span>
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<td class="old_line diff-line-num" data-linenumber="1201" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1201
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<td class="new_line diff-line-num" data-linenumber="1213" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1213
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<pre style="margin: 0;"> <span id="LC1213" class="line" lang="c"> <span class="n" style="color: #333;">ni</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="1202" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1202
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<td class="new_line diff-line-num" data-linenumber="1214" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1214
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<pre style="margin: 0;"> <span id="LC1214" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="n" style="color: #333;">nl</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;">nl</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">b</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">n_lines</span><span class="p">;</span><span class="n" style="color: #333;">nl</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="1203" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1203
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<td class="new_line diff-line-num" data-linenumber="1215" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1215
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<pre style="margin: 0;"> <span id="LC1215" class="line" lang="c"> <span class="n" style="color: #333;">line</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">b</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">l</span><span class="p">[</span><span class="n" style="color: #333;">nl</span><span class="p">]</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">line</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="1204" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1204
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<td class="new_line diff-line-num" data-linenumber="1216" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1216
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<pre style="margin: 0;"> <span id="LC1216" class="line" lang="c"> <span class="n" style="color: #333;">line_len</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">b</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">l</span><span class="p">[</span><span class="n" style="color: #333;">nl</span><span class="p">]</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">len</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="1205" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1205
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<td class="new_line diff-line-num" data-linenumber="1217" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1217
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<pre style="margin: 0;"> <span id="LC1217" class="line" lang="c"> <span class="n" style="color: #333;">ni</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 old" data-linenumber="1206" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1206
</td>
<td class="new_line diff-line-num old" data-linenumber="1218" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1206" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">//line_len = nread;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1207" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1207
</td>
<td class="new_line diff-line-num old" data-linenumber="1218" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1207" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">//line[line_len-1] = 0;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1208" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1208
</td>
<td class="new_line diff-line-num old" data-linenumber="1218" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1208" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* line_len--; */</span></span>
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<td class="old_line diff-line-num" data-linenumber="1209" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1209
</td>
<td class="new_line diff-line-num" data-linenumber="1218" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1218
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<pre style="margin: 0;"> <span id="LC1218" class="line" lang="c"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="1210" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1210
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<td class="new_line diff-line-num" data-linenumber="1219" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1219
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<pre style="margin: 0;"> <span id="LC1219" class="line" lang="c"> <span class="p">}</span></span>
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<td class="old_line diff-line-num" data-linenumber="1211" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1211
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<td class="new_line diff-line-num" data-linenumber="1220" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1220
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<pre style="margin: 0;"> <span id="LC1220" class="line" lang="c"> <span class="n" style="color: #333;">active_seq</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="1212" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1212
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<td class="new_line diff-line-num" data-linenumber="1221" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1221
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<pre style="margin: 0;"> <span id="LC1221" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="n" style="color: #333;">nl</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ni</span><span class="p">;</span> <span class="n" style="color: #333;">nl</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">b</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">n_lines</span><span class="p">;</span><span class="n" style="color: #333;">nl</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="1213" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1213
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<td class="new_line diff-line-num" data-linenumber="1222" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1222
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<pre style="margin: 0;"> <span id="LC1222" class="line" lang="c"> <span class="n" style="color: #333;">line</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">b</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">l</span><span class="p">[</span><span class="n" style="color: #333;">nl</span><span class="p">]</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">line</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="1214" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1214
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<td class="new_line diff-line-num" data-linenumber="1223" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1223
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<pre style="margin: 0;"> <span id="LC1223" class="line" lang="c"> <span class="n" style="color: #333;">line_len</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">b</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">l</span><span class="p">[</span><span class="n" style="color: #333;">nl</span><span class="p">]</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">len</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1215" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1215
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<td class="new_line diff-line-num old" data-linenumber="1224" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1215" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">//while ((nread = getline(&line, &b_len, f_ptr)) != -1){</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1216" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1216
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<td class="new_line diff-line-num old" data-linenumber="1224" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1216" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">//while(fgets(line, BUFFER_LEN, f_ptr)){</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1217" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1217
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<td class="new_line diff-line-num old" data-linenumber="1224" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1217" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">//line_len = strnlen(line, BUFFER_LEN);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1218" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1218
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<td class="new_line diff-line-num old" data-linenumber="1224" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1218" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">//line_len = nread;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1219" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1219
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<td class="new_line diff-line-num old" data-linenumber="1224" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1219" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">//line[line_len-1] = 0;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1220" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1220
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<td class="new_line diff-line-num old" data-linenumber="1224" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1220" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* line_len--; /\* last character is newline *\/ */</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1221" style="width: 35px; color: rgba(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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1224
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<pre style="margin: 0;">+<span id="LC1224" class="line" lang="c"></span>
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1221
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1225
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<pre style="margin: 0;"> <span id="LC1225" 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;">line_len</span><span class="p">){</span></span>
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1222
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<td class="new_line diff-line-num" data-linenumber="1226" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1226
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<pre style="margin: 0;"> <span id="LC1226" class="line" lang="c"> <span class="n" style="color: #333;">active_seq</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="1223" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1223
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<td class="new_line diff-line-num" data-linenumber="1227" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1227
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<pre style="margin: 0;"> <span id="LC1227" class="line" lang="c"> <span class="p">}</span><span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1226" style="width: 35px; color: rgba(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="1230" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1226,9 +1230,6 @@ int read_clu(struct in_buffer* b , struct msa** m)</td>
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<td class="old_line diff-line-num" data-linenumber="1226" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1226
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<td class="new_line diff-line-num" data-linenumber="1230" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1230
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<pre style="margin: 0;"> <span id="LC1230" class="line" lang="c"> <span class="n" style="color: #333;">RUN</span><span class="p">(</span><span class="n" style="color: #333;">resize_msa</span><span class="p">(</span><span class="n" style="color: #333;">msa</span><span class="p">));</span></span>
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1227
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1231
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<pre style="margin: 0;"> <span id="LC1231" class="line" lang="c"> <span class="p">}</span></span>
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1228
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<td class="new_line diff-line-num" data-linenumber="1232" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1232
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<pre style="margin: 0;"> <span id="LC1232" class="line" lang="c"> <span class="n" style="color: #333;">seq_ptr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">msa</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">sequences</span><span class="p">[</span><span class="n" style="color: #333;">active_seq</span><span class="p">];</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1229" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1229
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<td class="new_line diff-line-num old" data-linenumber="1233" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1229" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">//p = strstr(line,seq_ptr->name);</span></span>
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1230
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<pre style="margin: 0;">-<span id="LC1230" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">//if(p){</span></span>
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1231
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<pre style="margin: 0;">-<span id="LC1231" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">//LOG_MSG("Found bitsof seq %s", seq_ptr->name);</span></span>
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1232
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1233
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<pre style="margin: 0;"> <span id="LC1233" class="line" lang="c"></span>
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1233
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1234
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<pre style="margin: 0;"> <span id="LC1234" class="line" lang="c"> <span class="n" style="color: #333;">p</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">line</span><span class="p">;</span></span>
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1234
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1235
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<pre style="margin: 0;"> <span id="LC1235" class="line" lang="c"> <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>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1254" style="width: 35px; color: rgba(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="1255" style="width: 35px; color: rgba(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">@@ -1254,11 +1255,8 @@ int read_clu(struct in_buffer* b , struct msa** m)</td>
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1254
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1255
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<pre style="margin: 0;"> <span id="LC1255" class="line" lang="c"> <span class="p">}</span></span>
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1255
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<td class="new_line diff-line-num" data-linenumber="1256" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1256
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<pre style="margin: 0;"> <span id="LC1256" class="line" lang="c"> <span class="n" style="color: #333;">active_seq</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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1256
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<td class="new_line diff-line-num" data-linenumber="1257" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1257
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<pre style="margin: 0;"> <span id="LC1257" class="line" lang="c"> <span class="n" style="color: #333;">msa</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">numseq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">MACRO_MAX</span><span class="p">(</span><span class="n" style="color: #333;">msa</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">numseq</span><span class="p">,</span> <span class="n" style="color: #333;">active_seq</span><span class="p">);</span></span>
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1257
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<pre style="margin: 0;">-<span id="LC1257" class="line" lang="c"></span>
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1258
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1258
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<pre style="margin: 0;"> <span id="LC1258" class="line" lang="c"> <span class="p">}</span></span>
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1259
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<pre style="margin: 0;">-<span id="LC1259" class="line" lang="c"></span>
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1260
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1259
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<pre style="margin: 0;"> <span id="LC1259" class="line" lang="c"> <span class="p">}</span></span>
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1261
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<pre style="margin: 0;">-<span id="LC1261" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">//fprintf(stdout,"%d \"%s\"\n",line_len,line);</span></span>
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<td class="old_line diff-line-num" data-linenumber="1262" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1262
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1260
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<pre style="margin: 0;"> <span id="LC1260" class="line" lang="c"> <span class="p">}</span></span>
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1263
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1261
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<pre style="margin: 0;"> <span id="LC1261" class="line" lang="c"> <span class="n" style="color: #333;">RUN</span><span class="p">(</span><span class="n" style="color: #333;">null_terminate_sequences</span><span class="p">(</span><span class="n" style="color: #333;">msa</span><span class="p">));</span></span>
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1264
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1262
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<pre style="margin: 0;"> <span id="LC1262" class="line" lang="c"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1372" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1370" style="width: 35px; color: rgba(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">@@ -1372,35 +1370,19 @@ int read_fasta( struct in_buffer* b,struct msa** m)</td>
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1372
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1370
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<pre style="margin: 0;"> <span id="LC1370" class="line" lang="c"><span class="p">{</span></span>
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1373
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1371
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<pre style="margin: 0;"> <span id="LC1371" class="line" lang="c"> <span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">msa</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">msa</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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1374
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1372
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<pre style="margin: 0;"> <span id="LC1372" class="line" lang="c"> <span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">msa_seq</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">seq_ptr</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1375" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1375
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<td class="new_line diff-line-num old" data-linenumber="1373" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1375" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">//FILE* f_ptr = NULL;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1376" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1376
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<pre style="margin: 0;">-<span id="LC1376" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">line</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1377" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1377
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<pre style="margin: 0;">-<span id="LC1377" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">//size_t b_len = 0;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1378" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1378
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<td class="new_line diff-line-num old" data-linenumber="1373" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1378" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">//ssize_t nread;</span></span>
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1379
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1373
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<pre style="margin: 0;"> <span id="LC1373" class="line" lang="c"></span>
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<td class="old_line diff-line-num old" data-linenumber="1380" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1380
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<td class="new_line diff-line-num old" data-linenumber="1374" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1380" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left">//</span>char line<span class="idiff right">[BUFFER_LEN]</span>;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1374" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1374
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<pre style="margin: 0;">+<span id="LC1374" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;"><span class="idiff left">*</span></span> <span class="n" style="color: #333;">line</span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff right">NULL</span></span><span class="p">;</span></span>
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1381
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<td class="new_line diff-line-num" data-linenumber="1375" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1375
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<pre style="margin: 0;"> <span id="LC1375" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">line_len</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="1382" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1382
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<td class="new_line diff-line-num" data-linenumber="1376" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1376
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<pre style="margin: 0;"> <span id="LC1376" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="1383" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1383
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<td class="new_line diff-line-num" data-linenumber="1377" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1377
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<pre style="margin: 0;"> <span id="LC1377" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nl</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="1384" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1384
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<td class="new_line diff-line-num" data-linenumber="1378" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1378
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<pre style="margin: 0;"> <span id="LC1378" class="line" lang="c"></span>
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1385
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<td class="new_line diff-line-num old" data-linenumber="1379" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1385" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* sanity checks */</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1386" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1386
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<td class="new_line diff-line-num old" data-linenumber="1379" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1386" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">//if(!my_file_exists(infile)){</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1387" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1387
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<td class="new_line diff-line-num old" data-linenumber="1379" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1387" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">//ERROR_MSG("File: %s does not exist.",infile);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1388" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1388
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<td class="new_line diff-line-num old" data-linenumber="1379" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1388" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">//}</span></span>
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<td class="old_line diff-line-num" data-linenumber="1389" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1389
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<td class="new_line diff-line-num" data-linenumber="1379" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1379
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<pre style="margin: 0;"> <span id="LC1379" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">msa</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">){</span></span>
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<td class="old_line diff-line-num" data-linenumber="1390" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1390
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<td class="new_line diff-line-num" data-linenumber="1380" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1380
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<pre style="margin: 0;"> <span id="LC1380" class="line" lang="c"> <span class="n" style="color: #333;">msa</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alloc_msa</span><span class="p">();</span></span>
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<td class="old_line diff-line-num" data-linenumber="1391" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1391
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<td class="new_line diff-line-num" data-linenumber="1381" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1381
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<pre style="margin: 0;"> <span id="LC1381" class="line" lang="c"> <span class="p">}</span></span>
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1392
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<td class="new_line diff-line-num" data-linenumber="1382" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1382
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<pre style="margin: 0;"> <span id="LC1382" class="line" lang="c"></span>
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1393
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<td class="new_line diff-line-num old" data-linenumber="1383" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1393" class="line" lang="c"></span>
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<td class="old_line diff-line-num" data-linenumber="1394" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1394
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<td class="new_line diff-line-num" data-linenumber="1383" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1383
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<pre style="margin: 0;"> <span id="LC1383" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="n" style="color: #333;">nl</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;">nl</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">b</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">n_lines</span><span class="p">;</span><span class="n" style="color: #333;">nl</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="1395" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1395
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<td class="new_line diff-line-num" data-linenumber="1384" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1384
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<pre style="margin: 0;"> <span id="LC1384" class="line" lang="c"> <span class="n" style="color: #333;">line</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">b</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">l</span><span class="p">[</span><span class="n" style="color: #333;">nl</span><span class="p">]</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">line</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="1396" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1396
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<td class="new_line diff-line-num" data-linenumber="1385" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1385
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<pre style="margin: 0;"> <span id="LC1385" class="line" lang="c"> <span class="n" style="color: #333;">line_len</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">b</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">l</span><span class="p">[</span><span class="n" style="color: #333;">nl</span><span class="p">]</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">len</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1397" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1397
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<td class="new_line diff-line-num old" data-linenumber="1386" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1397" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">//RUNP(f_ptr = fopen(infile, "r"));</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1398" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1398
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<td class="new_line diff-line-num old" data-linenumber="1386" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1398" class="line" lang="c"></span>
</pre>
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<td class="old_line diff-line-num old" data-linenumber="1399" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1399
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<td class="new_line diff-line-num old" data-linenumber="1386" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1399" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">//while ((nread = getline(&line, &b_len, f_ptr)) != -1){</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1400" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1400
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<td class="new_line diff-line-num old" data-linenumber="1386" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1400" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">//while(fgets(line, BUFFER_LEN, f_ptr)){</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1401" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1401
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<td class="new_line diff-line-num old" data-linenumber="1386" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1401" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">//line_len = nread;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1402" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1402
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<td class="new_line diff-line-num old" data-linenumber="1386" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1402" class="line" lang="c"></span>
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1403
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<td class="new_line diff-line-num old" data-linenumber="1386" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1403" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">//fprintf(stdout,"%d %s\n",line_len,line);</span></span>
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<td class="old_line diff-line-num" data-linenumber="1404" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1404
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1386
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<pre style="margin: 0;"> <span id="LC1386" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">'>'</span><span class="p">){</span></span>
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1405
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<td class="new_line diff-line-num" data-linenumber="1387" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1387
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<pre style="margin: 0;"> <span id="LC1387" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* alloc seq if buffer is full */</span></span>
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<td class="old_line diff-line-num" data-linenumber="1406" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1406
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<td class="new_line diff-line-num" data-linenumber="1388" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1388
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<pre style="margin: 0;"> <span id="LC1388" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">msa</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">alloc_numseq</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">msa</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">numseq</span><span class="p">){</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1424" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1406" style="width: 35px; color: rgba(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">@@ -1424,12 +1406,11 @@ int read_fasta( struct in_buffer* b,struct msa** m)</td>
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1424
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1406
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<pre style="margin: 0;"> <span id="LC1406" 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;">seq_ptr</span><span class="p">){</span></span>
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<td class="old_line diff-line-num" data-linenumber="1425" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1425
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<td class="new_line diff-line-num" data-linenumber="1407" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1407
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<pre style="margin: 0;"> <span id="LC1407" class="line" lang="c"> <span class="n" style="color: #333;">ERROR_MSG</span><span class="p">(</span><span class="s" style="color: #d14;">"Encountered a sequence before encountering it's name"</span><span class="p">);</span></span>
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<td class="old_line diff-line-num" data-linenumber="1426" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1426
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<td class="new_line diff-line-num" data-linenumber="1408" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1408
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<pre style="margin: 0;"> <span id="LC1408" class="line" lang="c"> <span class="p">}</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1427" style="width: 35px; color: rgba(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="1409" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1409
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<pre style="margin: 0;">+<span id="LC1409" class="line" lang="c"> <span class="n" style="color: #333;">seq_ptr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seq</span><span class="p">[</span><span class="n" style="color: #333;">seq_ptr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">len</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">line</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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<td class="old_line diff-line-num new" data-linenumber="1427" style="width: 35px; color: rgba(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="1410" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1410
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<pre style="margin: 0;">+<span id="LC1410" class="line" lang="c"> <span class="n" style="color: #333;">seq_ptr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">len</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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1427
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<td class="new_line diff-line-num" data-linenumber="1411" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1411
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<pre style="margin: 0;"> <span id="LC1411" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">seq_ptr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">alloc_len</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">seq_ptr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">len</span><span class="p">){</span></span>
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<td class="old_line diff-line-num" data-linenumber="1428" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1428
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<td class="new_line diff-line-num" data-linenumber="1412" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1412
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<pre style="margin: 0;"> <span id="LC1412" class="line" lang="c"> <span class="n" style="color: #333;">resize_msa_seq</span><span class="p">(</span><span class="n" style="color: #333;">seq_ptr</span><span class="p">);</span></span>
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<td class="old_line diff-line-num" data-linenumber="1429" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1429
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<td class="new_line diff-line-num" data-linenumber="1413" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1413
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<pre style="margin: 0;"> <span id="LC1413" class="line" lang="c"> <span class="p">}</span></span>
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1430
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<td class="new_line diff-line-num old" data-linenumber="1414" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1430" class="line" lang="c"></span>
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<td class="old_line diff-line-num old" data-linenumber="1431" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1431
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<td class="new_line diff-line-num old" data-linenumber="1414" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1431" class="line" lang="c"> <span class="n" style="color: #333;">seq_ptr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seq</span><span class="p">[</span><span class="n" style="color: #333;">seq_ptr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">len</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">line</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1432" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1432
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<td class="new_line diff-line-num old" data-linenumber="1414" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1432" class="line" lang="c"> <span class="n" style="color: #333;">seq_ptr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">len</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="1433" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1433
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<td class="new_line diff-line-num" data-linenumber="1414" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1414
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<pre style="margin: 0;"> <span id="LC1414" class="line" lang="c"> <span class="p">}</span><span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">ispunct</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;">line</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">])){</span></span>
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<td class="old_line diff-line-num" data-linenumber="1434" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1434
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<td class="new_line diff-line-num" data-linenumber="1415" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1415
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<pre style="margin: 0;"> <span id="LC1415" class="line" lang="c"> <span class="n" style="color: #333;">seq_ptr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">gaps</span><span class="p">[</span><span class="n" style="color: #333;">seq_ptr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">len</span><span class="p">]</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="1435" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1435
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<td class="new_line diff-line-num" data-linenumber="1416" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1416
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<pre style="margin: 0;"> <span id="LC1416" 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="1440" style="width: 35px; color: rgba(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="1421" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1440,17 +1421,10 @@ int read_fasta( struct in_buffer* b,struct msa** m)</td>
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1440
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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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1441
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<td class="new_line diff-line-num" data-linenumber="1422" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1422
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<pre style="margin: 0;"> <span id="LC1422" class="line" lang="c"></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="1442" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1442
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<td class="new_line diff-line-num" data-linenumber="1423" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1423
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<pre style="margin: 0;"> <span id="LC1423" class="line" lang="c"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">m</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">msa</span><span class="p">;</span></span>
</pre>
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1443
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<td class="new_line diff-line-num old" data-linenumber="1424" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1443" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">//fclose(f_ptr);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1444" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1444
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<td class="new_line diff-line-num old" data-linenumber="1424" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1444" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">//MFREE(line);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1424" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1424
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<pre style="margin: 0;">+<span id="LC1424" class="line" lang="c"></span>
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<td class="old_line diff-line-num" data-linenumber="1445" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1445
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<td class="new_line diff-line-num" data-linenumber="1425" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1425
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<pre style="margin: 0;"> <span id="LC1425" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">OK</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="1446" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1446
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<td class="new_line diff-line-num" data-linenumber="1426" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1426
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1426" class="line" lang="c"><span class="nl">ERROR:</span></span>
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<td class="old_line diff-line-num" data-linenumber="1447" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1447
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<td class="new_line diff-line-num" data-linenumber="1427" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1427
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<pre style="margin: 0;"> <span id="LC1427" class="line" lang="c"> <span class="n" style="color: #333;">free_msa</span><span class="p">(</span><span class="n" style="color: #333;">msa</span><span class="p">);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1448" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1448
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<td class="new_line diff-line-num old" data-linenumber="1428" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1448" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">//if(line){</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1449" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1449
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<td class="new_line diff-line-num old" data-linenumber="1428" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1449" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">//MFREE(line);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1450" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1450
</td>
<td class="new_line diff-line-num old" data-linenumber="1428" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1450" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">//}</span></span>
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1451
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<td class="new_line diff-line-num old" data-linenumber="1428" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1451" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">//if(f_ptr){</span></span>
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1452
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<td class="new_line diff-line-num old" data-linenumber="1428" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1452" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">//fclose(f_ptr);</span></span>
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<td class="old_line diff-line-num old" data-linenumber="1453" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1453
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<td class="new_line diff-line-num old" data-linenumber="1428" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1453" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">//}</span></span>
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<td class="old_line diff-line-num" data-linenumber="1454" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1454
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<td class="new_line diff-line-num" data-linenumber="1428" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1428
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<pre style="margin: 0;"> <span id="LC1428" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">FAIL</span><span class="p">;</span></span>
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<td class="old_line diff-line-num" data-linenumber="1455" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1455
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1429
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<pre style="margin: 0;"> <span id="LC1429" class="line" lang="c"><span class="p">}</span></span>
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1456
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<td class="new_line diff-line-num" data-linenumber="1430" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1430
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<pre style="margin: 0;"> <span id="LC1430" class="line" lang="c"></span>
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<a href="https://salsa.debian.org/med-team/kalign/-/commit/7ebdac5ad2b6823ab8972de5e525d333aa9b4d51#fc361d05a36c44f4d7065a69f501c01dd8628237"><strong>src/weave_alignment.c</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="28" style="width: 35px; color: rgba(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="28" style="width: 35px; color: rgba(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">@@ -28,32 +28,6 @@</td>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">//int update_gaps(int old_len,int*gis,int new_len,int *newgaps);</span></span>
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29
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29
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">update_gaps</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">old_len</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;">gis</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;">newgaps</span><span class="p">);</span></span>
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30
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30
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="c"></span>
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31
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">weave</span><span class="p">(</span><span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">msa</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">msa</span><span class="p">,</span><span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">aln_tasks</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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32
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="c"><span class="p">{</span></span>
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33
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">a</span><span class="p">,</span><span class="n" style="color: #333;">b</span><span class="p">,</span><span class="n" style="color: #333;">c</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="c1" style="color: #998; font-style: italic;">//RUN(clean_aln(aln)</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="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;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">t</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">n_tasks</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>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="c"> <span class="n" style="color: #333;">a</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">t</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">list</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">a</span><span class="p">;</span></span>
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40
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="c"> <span class="n" style="color: #333;">b</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">t</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">list</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">b</span><span class="p">;</span></span>
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41
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="c"> <span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">t</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">list</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">c</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* fprintf(stdout,"%3d %3d -> %3d (p: %d)\n", t->list[i]->a, t->list[i]->b, t->list[i]->c, t->list[i]->p); */</span></span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* RUN(make_seq(msa,a,b,t->map[c])); */</span></span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="c"> <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="cm" style="color: #998; font-style: italic;">/*for (i = 0; i < (msa->numseq-1)*3;i +=3){</span></span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> a = tree[i];</span></span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> b = tree[i+1];</span></span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> RUN(make_seq(msa,a,b,map[tree[i+2]]));</span></span>
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50
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> }*/</span></span>
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51
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="c"></span>
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52
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">OK</span><span class="p">;</span></span>
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53
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="c"><span class="nl">ERROR:</span></span>
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54
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">FAIL</span><span class="p">;</span></span>
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55
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="c"><span class="p">}</span></span>
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56
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<pre style="margin: 0;">-<span id="LC56" 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;">int</span> <span class="nf" style="color: #900; font-weight: 600;">clean_aln</span><span class="p">(</span><span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">msa</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">msa</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="c"><span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC33" 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>
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<a href="https://salsa.debian.org/med-team/kalign/-/commit/7ebdac5ad2b6823ab8972de5e525d333aa9b4d51#86c2e400778487ece9407ed83a97fc3900542320"><strong>src/weave_alignment.h</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -29,7 +29,7 @@</td>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">//extern int weave(struct msa* msa, int** map, int* tree);</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="k" style="font-weight: 600;">extern</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">weave</span><span class="p">(</span><span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;"><span class="idiff left">msa</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">msa</span></span><span class="p"><span class="idiff">,</span></span><span class="k" style="font-weight: 600;"><span class="idiff">struct</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">aln_tasks</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">t</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"><span class="idiff left">/* </span>extern int weave(struct aln_tasks*<span class="idiff"> </span>t);<span class="idiff right"> */</span></span></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="c"><span class="k" style="font-weight: 600;">extern</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">make_seq</span><span class="p">(</span><span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">msa</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">msa</span><span class="p">,</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">a</span><span class="p">,</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">b</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;">path</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="c"><span class="k" style="font-weight: 600;">extern</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">clean_aln</span><span class="p">(</span><span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">msa</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">msa</span><span class="p">);</span></span>
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