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<h3>
Steffen Möller pushed to branch master
at <a href="https://salsa.debian.org/med-team/lagan">Debian Med / lagan</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/lagan/commit/690c74bd2f44de1a70375de1107789db15357798">690c74bd</a></strong>
<div>
<span>by Steffen Moeller</span>
<i>at 2018-09-07T13:17:36Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Preparing for upload to experimental.
</pre>
</li>
</ul>
<h4>13 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
</a>
</li>
<li class="file-stats">
<a href="#adb7f75f79e3bb85eb62912a2904c5d24af878fb">
debian/copyright
</a>
</li>
<li class="file-stats">
<a href="#9a14945e16c9144bd18a7ed182b1f8e4a2b50d7c">
<span class="new-file">
+
debian/examples
</span>
</a>
</li>
<li class="file-stats">
<a href="#c3289b46eb4b28abb37a76fcdb3184bad7dfd578">
debian/install
→
debian/lagan.install
</a>
</li>
<li class="file-stats">
<a href="#afa358388fe07ab6e69a75b20f9bfb8728060a5a">
<span class="new-file">
+
debian/lagan.lintian-overrides
</span>
</a>
</li>
<li class="file-stats">
<a href="#68e0b13744e158347bfd74ebaaca667435f07d14">
<span class="new-file">
+
debian/manpages
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</a>
</li>
<li class="file-stats">
<a href="#5cf099c5f16936c89fac10631939c4b132c8ccdb">
<span class="new-file">
+
debian/mlagan.1
</span>
</a>
</li>
<li class="file-stats">
<a href="#60d4e840e5dcc9dd829597f6a0c2c064ba5ea937">
<span class="new-file">
+
debian/patches/addTest.patch
</span>
</a>
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<li class="file-stats">
<a href="#b76dfe8feb298c3fbfffad72e8b494f83e310c1d">
<span class="new-file">
+
debian/patches/adjustPerlPaths.patch
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<li class="file-stats">
<a href="#6752da3cd15fa35e515104055ac0f4f10824e2cb">
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+
debian/patches/ambiuousEnd.patch
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</a>
</li>
<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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</li>
<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/lagan/commit/690c74bd2f44de1a70375de1107789db15357798#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">lagan (2.0-2) experimental; urgency=low</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * Initial release to experimental to invite peer review (Closes: #908215).</span>
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<td class="diff-line-num new new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * Added man page for mlagan, also added *.pl scripts to /usr/bin</span>
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<td class="diff-line-num new new_line" data-linenumber="5" style="width: 35px; color: rgba(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="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> * Added embarrassingly simple test routine to run "mlagan -h"</span>
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<td class="diff-line-num new new_line" data-linenumber="6" style="width: 35px; color: rgba(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="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> * Solved compile time "ambiguity" error</span>
</pre>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> * d/control:</span>
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<td class="diff-line-num new new_line" data-linenumber="8" style="width: 35px; color: rgba(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="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> - Bumped policy to 4.2.1</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> - Adjusted URLs to repository</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> * d/changelog: updated GSF address</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> * lintian overrides for .pl endings</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> -- Steffen Moeller <moeller@debian.org> Fri, 07 Sep 2018 14:10:07 +0200</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"></span>
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<td class="diff-line-num new_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">lagan (2.0-1) UNRELEASED; urgency=low</span>
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<td class="diff-line-num new_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext"> * Initial release</span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext"> * TODO:</span>
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<td class="diff-line-num old_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext"> - fix installation location possibly wrapper script featuring</span>
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<td class="diff-line-num old_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext"> some $lagandir path variable (/usr/lib/lagan ???)</span>
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</li>
<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/lagan/commit/690c74bd2f44de1a70375de1107789db15357798#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">Source: lagan</span>
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org></span>
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3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">Uploaders: Andreas Tille <tille@debian.org></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">Uploaders: Andreas Tille <tille@debian.org><span class="idiff left right">, Steffen Moeller <moeller@debian.org></span></span>
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4
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">Section: science</span>
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Priority: optional</span>
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6
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Build-Depends: debhelper (>= 10),</span>
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<td class="diff-line-num old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7
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<td class="diff-line-num new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"> libboost-dev</span>
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8
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">1</span>.1</span>
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<td class="diff-line-num old old_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
9
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<td class="diff-line-num new_line old" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext">Vcs-Browser: https://<span class="idiff left right">anonscm.debian.org/cgit/debian-med/lagan.git</span></span>
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10
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext">Vcs-Git: https://<span class="idiff left right">anonscm.debian.org/git/debian-med</span>/lagan.git</span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">2</span>.1</span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">Vcs-Browser: https://<span class="idiff left right">salsa.debian.org/med-team/lagan</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">Vcs-Git: https://<span class="idiff left right">salsa.debian.org/med-team</span>/lagan.git</span>
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11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">Homepage: http://lagan.stanford.edu/lagan_web/index.shtml</span>
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<td class="diff-line-num old_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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">Package: lagan</span>
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<td class="diff-line-num old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
14
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">Architecture: any</span>
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<td class="diff-line-num old_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">Depends: ${shlibs:Depends},</span>
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<td class="diff-line-num old_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
16
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"> ${misc:Depends}</span>
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17
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="plaintext">Description: highly parametrizable pairwise global <span class="idiff left right">alignment program</span></span>
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<td class="diff-line-num new old_line" data-linenumber="18" style="width: 35px; color: rgba(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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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">Description: highly parametrizable pairwise global <span class="idiff left right">genome sequence aligner</span></span>
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<td class="diff-line-num old_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
18
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext"> Lagan takes local alignments generated by CHAOS as anchors, and limits</span>
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<td class="diff-line-num old_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
19
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext"> the search area of the Needleman-Wunsch algorithm around these anchors.</span>
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20
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext"> .</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">@@ -7,26 +7,25 @@ Files-Excluded:</td>
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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">Files: *</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">Copyright: © 2003-2006 Michael Brudno, Chuong Do, et. al.</span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext">License: GPL<span class="idiff left right">v2</span>+</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">License: GPL<span class="idiff left right">-2.0</span>+</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">Files: debian/*</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">Copyright: © 2012-2013 Andreas Tille <tille@debian.org></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext">License: GPL<span class="idiff left right">v2</span>+</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">License: GPL<span class="idiff left right">-2.0</span>+</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="plaintext">License: GPL<span class="idiff left right">v2</span>+</span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="plaintext"> <span class="idiff left right"> This program</span> is free software; you can redistribute it and/or modify</span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="plaintext"> <span class="idiff left right"> </span>it under the terms of the GNU General Public License as published by</span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="plaintext"> <span class="idiff left right"> </span>the Free Software Foundation; either version 2 of the License, or</span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="plaintext"> <span class="idiff left right"> </span>(at your option) any later version.</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">License: GPL<span class="idiff left right">-2.0</span>+</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"> <span class="idiff left right">This package</span> is free software; you can redistribute it and/or modify</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"> it under the terms of the GNU General Public License as published by</span>
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<pre style="margin: 0;">+<span id="LC19" 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="LC20" class="line" lang="plaintext"> (at your option) any later version.</span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="plaintext"> <span class="idiff left right"> This program</span> is distributed in the hope that it will be useful,</span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="plaintext"> <span class="idiff left right"> </span>but WITHOUT ANY WARRANTY; without even the implied warranty of</span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="plaintext"> <span class="idiff left right"> </span>MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the</span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="plaintext"> <span class="idiff left right"> </span>GNU General Public License for more details.</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"> <span class="idiff left right">This package</span> is distributed in the hope that it will be useful,</span>
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<pre style="margin: 0;">+<span id="LC23" 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="LC24" class="line" lang="plaintext"> MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext"> GNU General Public License for more details.</span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;">-<span id="LC27" 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="LC28" 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="LC29" 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="LC27" 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="LC28" 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="LC29" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="plaintext"> On Debian systems<span class="idiff left right"> you can find the full text of the GPL 2+ license</span></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="plaintext"> <span class="idiff left right">at /usr/share/common-licenses/GPL-2</span>.</span></pre>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext"> On Debian systems<span class="idiff left right">, the complete text of the GNU General</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext"> <span class="idiff left right">Public License version 2 can be found in "/usr/share/common-licenses/GPL-2"</span>.</span></pre>
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<a href="https://salsa.debian.org/med-team/lagan/commit/690c74bd2f44de1a70375de1107789db15357798#9a14945e16c9144bd18a7ed182b1f8e4a2b50d7c"><strong>debian/examples</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">sample.fasta</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">sample.params</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">test.score</span></pre>
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<a href="https://salsa.debian.org/med-team/lagan/commit/690c74bd2f44de1a70375de1107789db15357798#c3289b46eb4b28abb37a76fcdb3184bad7dfd578"><strong>debian/install</strong>
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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">@@ -2,5 +2,10 @@ anchors usr/bin</td>
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="php"><span class="nx">chaos</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">bin</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="php"><span class="nx">glocal</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">bin</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="php"><span class="nx">mlagan</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">bin</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="php"><span class="nx">prolagan</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">bin</span></span>
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5
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="php"><span class="nx">order</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">bin</span></span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="php"><span class="o" style="font-weight: 600;">*.</span><span class="nx">pl</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">bin</span></span>
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6
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<td class="diff-line-num new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
8
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="php"><span class="nx">utils</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">lib</span><span class="o" style="font-weight: 600;">/</span><span class="nx">lagan</span></span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="php"><span class="nx">blosum62s</span><span class="o" style="font-weight: 600;">.</span><span class="nx">txt</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">lib</span><span class="o" style="font-weight: 600;">/</span><span class="nx">lagan</span></span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="php"><span class="nx">blosum62</span><span class="o" style="font-weight: 600;">.</span><span class="nx">txt</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">lib</span><span class="o" style="font-weight: 600;">/</span><span class="nx">lagan</span></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="php"><span class="nx">nucmatrix</span><span class="o" style="font-weight: 600;">.</span><span class="nx">txt</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">lib</span><span class="o" style="font-weight: 600;">/</span><span class="nx">lagan</span></span></pre>
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<li id="afa358388fe07ab6e69a75b20f9bfb8728060a5a">
<a href="https://salsa.debian.org/med-team/lagan/commit/690c74bd2f44de1a70375de1107789db15357798#afa358388fe07ab6e69a75b20f9bfb8728060a5a"><strong>debian/lagan.lintian-overrides</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext"># Not messing with whatever defaults the community has already</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"># established for maximal compatibility with existing scripts.</span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">lagan: script-with-language-extension usr/bin/anal_gloc.pl</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">lagan: script-with-language-extension usr/bin/lagan.pl</span>
</pre>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">lagan: script-with-language-extension usr/bin/rechaos.pl</span>
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<td class="diff-line-num new new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">lagan: script-with-language-extension usr/bin/slagan-mfa.pl</span>
</pre>
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7
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">lagan: script-with-language-extension usr/bin/slagan.pl</span>
</pre>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">lagan: script-with-language-extension usr/bin/supermap.pl</span>
</pre>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">lagan: script-with-language-extension usr/bin/xmfa2mfa.pl</span>
</pre>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">lagan: binary-without-manpage usr/bin/anal_gloc.pl</span>
</pre>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">lagan: binary-without-manpage usr/bin/anchors</span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">lagan: binary-without-manpage usr/bin/chaos</span>
</pre>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">lagan: binary-without-manpage usr/bin/glocal</span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">lagan: binary-without-manpage usr/bin/lagan.pl</span>
</pre>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">lagan: binary-without-manpage usr/bin/order</span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">lagan: binary-without-manpage usr/bin/prolagan</span>
</pre>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">lagan: binary-without-manpage usr/bin/rechaos.pl</span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">lagan: binary-without-manpage usr/bin/slagan-mfa.pl</span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">lagan: binary-without-manpage usr/bin/slagan.pl</span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">lagan: binary-without-manpage usr/bin/supermap.pl</span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">lagan: binary-without-manpage usr/bin/xmfa2mfa.pl</span></pre>
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<a href="https://salsa.debian.org/med-team/lagan/commit/690c74bd2f44de1a70375de1107789db15357798#68e0b13744e158347bfd74ebaaca667435f07d14"><strong>debian/manpages</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">debian/mlagan.1</span></pre>
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<a href="https://salsa.debian.org/med-team/lagan/commit/690c74bd2f44de1a70375de1107789db15357798#5cf099c5f16936c89fac10631939c4b132c8ccdb"><strong>debian/mlagan.1</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">.TH MLAGAN "1" "September 2018" "mlagan" "User Commands"</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">.SH NAME</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">mlagan \- highly parametrizable pairwise global aligner</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">.SH SYNOPSIS</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">mlagan seqfile_1 seqfile_2 [... seqfile_63] [-parameters]</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">.SH DESCRIPTION</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">Lagan takes local alignments generated by CHAOS as anchors, and limits</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">the search area of the Needleman-Wunsch algorithm around these anchors.</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">.PP</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">Multi-LAGAN is a generalization of the pairwise algorithm to multiple</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">sequence alignment. M-LAGAN performs progressive pairwise alignments,</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">guided by a user-specified phylogenetic tree. Alignments are aligned to</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">other alignments using the sum-of-pairs metric.</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">.SH OPTIONS</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">.TP</span>
</pre>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">\fB\-nested\fR : runs improvement in a nested fashion</span>
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<td class="diff-line-num new new_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">\fB\-postir\fR : incorporates the final improvement phase</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">.TP</span>
</pre>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">\fB\-lazy\fR : uses lazy mode</span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">.TP</span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">\fB\-translate\fR : use translated anchors</span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">\fB\-fastreject\fR : use fast rejection (tuned for human/mouse or closer)</span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">.TP</span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">\fB\-verbose\fR : give debug output</span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">\fB\-tree\fR "(...)" : runs with given phylogenetic tree</span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">\fB\-out\fR "filename": outputs to filename</span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">\fB\-nucmatrixfile\fR "filename": uses given substitution matrix instead of \fI\,$LAGAN_DIR/nucmatrix.txt\/\fP</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext">\fB\-version\fR : prints version info</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext">.PP</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext">\fB\-nested\fR : runs improvement in a nested fashion</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext">\fB\-postir\fR : incorporates the final improvement phase</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext">\fB\-lazy\fR : uses lazy mode</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext">\fB\-translate\fR : use translated anchors</span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext">\fB\-fastreject\fR : use fast rejection (tuned for human/mouse or closer)</span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext">\fB\-verbose\fR : give debug output</span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext">\fB\-tree\fR "(...)" : runs with given phylogenetic tree</span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext">\fB\-out\fR "filename": outputs to filename</span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext">\fB\-nucmatrixfile\fR "filename": uses given substitution matrix instead of \fI\,$LAGAN_DIR/nucmatrix.txt\/\fP</span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext">\fB\-version\fR : prints version info</span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext">.SH ENVIRONMENT</span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="plaintext">The LAGAN_DIR variable specifies the location of the nucmatrix file. It</span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="plaintext">defaults to /usr/lib/lagan, where Debian also place that file.</span></pre>
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</li>
<li id="60d4e840e5dcc9dd829597f6a0c2c064ba5ea937">
<a href="https://salsa.debian.org/med-team/lagan/commit/690c74bd2f44de1a70375de1107789db15357798#60d4e840e5dcc9dd829597f6a0c2c064ba5ea937"><strong>debian/patches/addTest.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="gh" style="color: #999;">Index: lagan/Makefile</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- lagan.orig/Makefile</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ lagan/Makefile</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1,5 +1,8 @@</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"> all:</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- (cd src; $(MAKE))</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ $(MAKE) -C src</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> clean:</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> rm -f chaos anchors order glocal utils/bin2bl mlagan utils/cstat utils/bin2mf utils/rc *~ utils/contigorder utils/getbounds utils/cextract utils/seqmerge utils/getlength utils/getoverlap utils/*~ utils/scorealign utils/scorecontigs mlagan.purify utils/getcontigpos utils/fa2xfa utils/Glue utils/dotplot utils/overlay</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- (cd src; $(MAKE) clean)</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ $(MAKE) -C src clean</span></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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<td class="diff-line-num new new_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+test: all</span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ (LAGAN_DIR="." ./mlagan -h || true) | grep -q version && echo "[ok]" || echo "[fail]"</span></span></pre>
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<li id="b76dfe8feb298c3fbfffad72e8b494f83e310c1d">
<a href="https://salsa.debian.org/med-team/lagan/commit/690c74bd2f44de1a70375de1107789db15357798#b76dfe8feb298c3fbfffad72e8b494f83e310c1d"><strong>debian/patches/adjustPerlPaths.patch</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="gh" style="color: #999;">Index: lagan/anal_gloc.pl</span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- lagan.orig/anal_gloc.pl</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ lagan/anal_gloc.pl</span></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1,4 +1,4 @@</span></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env perl</span></span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/perl</span></span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> </span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> $savname1 = "";</span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> $savname2 = "";</span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="gh" style="color: #999;">Index: lagan/lagan.pl</span></span>
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<td class="diff-line-num new new_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
</pre>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- lagan.orig/lagan.pl</span></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ lagan/lagan.pl</span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1,4 +1,4 @@</span></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env perl</span></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/perl</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"> </span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> $lagandir = $ENV{LAGAN_DIR};</span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> $consrate = 45;</span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"><span class="gh" style="color: #999;">Index: lagan/rechaos.pl</span></span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- lagan.orig/rechaos.pl</span></span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ lagan/rechaos.pl</span></span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1,4 +1,4 @@</span></span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env perl</span></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/perl</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"> $lagandir = $ENV{LAGAN_DIR};</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"><span class="gh" style="color: #999;">Index: lagan/utils/cmerge2.pl</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- lagan.orig/utils/cmerge2.pl</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ lagan/utils/cmerge2.pl</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env perl</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/perl</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"> use File::Basename;</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"> $lagandir = $ENV{LAGAN_DIR};</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"><span class="gh" style="color: #999;">Index: lagan/utils/draft.pl</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- lagan.orig/utils/draft.pl</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ lagan/utils/draft.pl</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env perl</span></span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/perl</span></span>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"> use File::Basename;</span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"> </span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"> $lazyflag = 0;</span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"><span class="gh" style="color: #999;">Index: lagan/utils/mextract.pl</span></span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- lagan.orig/utils/mextract.pl</span></span>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ lagan/utils/mextract.pl</span></span>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1,4 +1,4 @@</span></span>
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env perl</span></span>
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/perl</span></span>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="diff"> </span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="diff"> if (@ARGV < 1) {</span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="diff"> print ("usage:\n mextract.pl filename [-masked]\n");</span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="diff"><span class="gh" style="color: #999;">Index: lagan/utils/mf2bin.pl</span></span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- lagan.orig/utils/mf2bin.pl</span></span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ lagan/utils/mf2bin.pl</span></span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1,4 +1,4 @@</span></span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env perl</span></span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/perl</span></span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="diff"> # defaults </span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="diff"> # constants</span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="diff"><span class="gh" style="color: #999;">Index: lagan/utils/mpretty.pl</span></span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- lagan.orig/utils/mpretty.pl</span></span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ lagan/utils/mpretty.pl</span></span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1,4 +1,4 @@</span></span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env perl</span></span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/perl</span></span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="diff"> </span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="diff"> # defaults </span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="diff"> </span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="diff"><span class="gh" style="color: #999;">Index: lagan/utils/mproject.pl</span></span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- lagan.orig/utils/mproject.pl</span></span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ lagan/utils/mproject.pl</span></span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1,4 +1,4 @@</span></span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env perl</span></span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/perl</span></span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="diff"> </span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="diff"> if (@ARGV < 2) {</span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="diff"> print ("usage:\n mproject.pl filename seqname1 [seqname2 ... ]\n");</span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="diff"><span class="gh" style="color: #999;">Index: lagan/utils/mrun.pl</span></span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- lagan.orig/utils/mrun.pl</span></span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ lagan/utils/mrun.pl</span></span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1,4 +1,4 @@</span></span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env perl</span></span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/perl</span></span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="diff"> </span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="diff"> # This script requires the environment variables:</span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="diff"> # LAGAN_DIR and VISTA_DIR</span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="diff"><span class="gh" style="color: #999;">Index: lagan/utils/mrunfile.pl</span></span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- lagan.orig/utils/mrunfile.pl</span></span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ lagan/utils/mrunfile.pl</span></span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1,4 +1,4 @@</span></span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env perl</span></span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/perl</span></span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="diff"> </span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="diff"> # This script requires the environment variables:</span>
</pre>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="diff"> # LAGAN_DIR and VISTA_DIR</span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="diff"><span class="gh" style="color: #999;">Index: lagan/utils/mrunpairs.pl</span></span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- lagan.orig/utils/mrunpairs.pl</span></span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ lagan/utils/mrunpairs.pl</span></span>
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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1,4 +1,4 @@</span></span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env perl</span></span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/perl</span></span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="diff"> </span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="diff"> # This script requires the environment variables:</span>
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="diff"> # LAGAN_DIR and VISTA_DIR</span>
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="diff"><span class="gh" style="color: #999;">Index: lagan/utils/msplit.pl</span></span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- lagan.orig/utils/msplit.pl</span></span>
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124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ lagan/utils/msplit.pl</span></span>
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125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1,4 +1,4 @@</span></span>
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126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env perl</span></span>
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127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/perl</span></span>
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128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="diff"> </span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="diff"> if (@ARGV < 1) {</span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="diff"> print ("usage:\n msplit.pl filename [-masked]\n");</span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="diff"><span class="gh" style="color: #999;">Index: lagan/utils/mviz.pl</span></span>
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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- lagan.orig/utils/mviz.pl</span></span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ lagan/utils/mviz.pl</span></span>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1,4 +1,4 @@</span></span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env perl</span></span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/perl</span></span>
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="diff"> </span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="diff"> </span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="diff"> # This script requires the environment variables:</span>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="diff"><span class="gh" style="color: #999;">Index: lagan/utils/Utils.pm</span></span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- lagan.orig/utils/Utils.pm</span></span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ lagan/utils/Utils.pm</span></span>
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1,5 +1,3 @@</span></span>
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146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env perl</span></span>
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="diff"> package Utils;</span>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="diff"> require 5.000;</span>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="diff"> </span></pre>
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<li id="6752da3cd15fa35e515104055ac0f4f10824e2cb">
<a href="https://salsa.debian.org/med-team/lagan/commit/690c74bd2f44de1a70375de1107789db15357798#6752da3cd15fa35e515104055ac0f4f10824e2cb"><strong>debian/patches/ambiuousEnd.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="gh" style="color: #999;">Index: lagan/src/glocal/rightinfluence.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- lagan.orig/src/glocal/rightinfluence.cpp</span></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ lagan/src/glocal/rightinfluence.cpp</span></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1,6 +1,6 @@</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"> #include <rightinfluence.h></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-Fragment origin, end;</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+static Fragment originFrag, endFrag;</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> // Sets the first default owner of the whole region</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> void initRI(RI *RightInfluence, long long int scoreIndex) {</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -13,22 +13,22 @@ void initRI(RI *RightInfluence, long lon</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> // will lose to anyone</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- origin.seq1End = 0; origin.seq2End = 0;</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- origin.seq1Start = 0; origin.seq2Start = 0;</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ originFrag.seq1End = 0; originFrag.seq2End = 0;</span></span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ originFrag.seq1Start = 0; originFrag.seq2Start = 0;</span></span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"> </span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"> // hack to aid winner selection</span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- origin.score = -1;</span></span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- end.score = -2;</span></span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- origin.totalScore = end.totalScore = 0;</span></span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ originFrag.score = -1;</span></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ endFrag.score = -2;</span></span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ originFrag.totalScore = endFrag.totalScore = 0;</span></span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"> </span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"> // will win against anyone</span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- end.seq1End = 0; end.seq2End = 0;</span></span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- end.seq1Start = 0; end.seq2Start = 0;</span></span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ endFrag.seq1End = 0; endFrag.seq2End = 0;</span></span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ endFrag.seq1Start = 0; endFrag.seq2Start = 0;</span></span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"> </span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- origin.back = NULL;</span></span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ originFrag.back = NULL;</span></span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- RightInfluence->act[-INF] = &origin;</span></span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- RightInfluence->act[+INF] = &end;</span></span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ RightInfluence->act[-INF] = &originFrag;</span></span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ RightInfluence->act[+INF] = &endFrag;</span></span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"> }</span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"> </span>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"> </span></pre>
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<a href="https://salsa.debian.org/med-team/lagan/commit/690c74bd2f44de1a70375de1107789db15357798#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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1
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">do_not_define_conflicting_getline.patch</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">gcc-4.8.patch</span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">ambiuousEnd.patch</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">addTest.patch</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">adjustPerlPaths.patch</span></pre>
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<a href="https://salsa.debian.org/med-team/lagan/commit/690c74bd2f44de1a70375de1107789db15357798#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -8,3 +8,7 @@</td>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">get-orig-source:</span>
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> mkdir -p ../tarballs</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> uscan --verbose --force-download --repack-compression xz --destdir=../tarballs</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">override_dh_auto_clean:</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> dh_auto_clean</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> rm -f prolagan</span></pre>
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